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In Attack of the Clones, Yoda says
Victory? Victory you say? Master Obi-Wan, not victory. The shroud of the dark side has fallen. Begun the Clone War has.
It's an epic Yoda line, and I get the need to set up continuity with A New Hope. But in-universe, it seems a little strange. Why does Yoda call it "The Clone War" after only one skirmish?
Does he have a premonition of the events to come? In which case, why didn't he warn someone?
In answer to why Yoda felt that it was only the beginning of a long-term engagement (Richard gives an excellent answer as to why Yoda named it specifically after the clones), even though Yoda did possess the ability to see into the future through the Force, the events preceding the First Battle of Geonosis on their own indicated that the battle was only the beginning:
At the time, The Republic/Jedi Council were already aware of the agglomeration of secession and dissent in the form of the Confederacy of Independent Systems as an ongoing and growing problem. The Separatist Crisis had been going on for over 10 years before the Clone Wars began (in 22 BBY), and its roots went back even further.
The Invasion of Naboo in 32 BBY revealed that the Trade Federation had prepared in secret, and was in possession of, a droid army, and was willing to use it.
Even though they had not taken it seriously at the time, many Jedi and others in the Republic had felt the approach of conflict, including Sifo-Dyas. Yoda had been in attendance of a meeting on just that topic in 32 BBY.
The attack by Darth Maul on Qui-gon's party (including then-Queen Amidala) in 32 BBY on Tatooine revealed the re-emergence of the Sith coterminous with the Invasion of Naboo.
After the death of Qui-gon Jinn in 32 BBY, Count Dooku left the Jedi Order to nominally lead what would become the CIS, culminating in the capture of Anakin Skywalker and Obi-wan Kenobi on Geonosis in 22 BBY, revealing himself fully to Kenobi as its martial leader and also revealing the existence of Darth Sidious and implying that the Republic itself was already internally at war and in peril. He also mentioned that the Trade Federation had been in league with this Sith Lord, tying the Sith with the Separatist Crisis.
The revelation on Kamino, and the mystery surrounding, the genesis of the clone army itself, and that it was apparently ordered for the Republic by Master Sifo-Dyas (a close former friend of Count Dooku). Jango Fett told Kenobi that he had been hired by a guy called Tyranus (not Darth Tyranus), and then later on in the execution arena on Geonosis in ATOTC, Jango was seen standing next to Dooku, the leader of the CIS.
Before Obi-wan Kenobi was captured on Geonosis, he transmitted (via Anakin/R2D2), a message to the Republic/Jedi, as follows:
I have tracked the bounty hunter Jango Fett to the droid foundries on Geonosis. The Trade Federation is to take delivery of a droid army here, and it is clear that Viceroy Gunray is behind the assassination attempts on Senator Amidala. The Commerce Guilds and the Corporate Alliance have both pledged their armies to Count Dooku and are forming a ... wait, wait ... (Kenobi is attacked by droids)
Two years before the First Battle of Geonosis, the Republic had proposed the Military Creation Act in response to the above-mentioned problems. The Act was passed in 22 BBY right after Kenobi's transmission, when (junior) Representative Jar Jar Binks, in place of Senator Amidala, proposed that Chancellor Palpatine be given emergency powers. Palpatine immediately used these powers to authorise said Act, whose first consequence was the clone army going to Geonosis along with the Jedi to help rescue Obi-wan (and the now-captured Anakin) and engage the Trade Federation/CIS.
Count Dooku revealed himself as, at the very least, a dark side practitioner, in his battle with Anakin/Obi-wan and then with Yoda on Geonosis. Yoda stated that he sensed the dark side in him, and he was using a red lightsaber, even though he still referred to himself as a Jedi. This, combined with what the Jedi had learned about the Sith and Yoda's own quote in the OP about the dark side descending, would add to the penumbra of war.
All of this is knowledge that Yoda presumably would have had before he made that comment at the end of ATOTC.
Note: This thread can also provide supplemental information.
Based on the Star Wars: Attack of the Clones: Junior Novelisation (by Patricia Wrede) we can actually get a pretty good understanding of Yoda's thought process when he comes up with the name:
They had lost so many Jedi. Two hundred had gone to Geonosis; barely twenty had returned. Still, they had won. “I have to admit, without the clones it would not have been a victory,” Obi-Wan said.
“Victory?” Yoda sat indignantly upright in his chair. “Victory, you say?” Obi-Wan turned. Yoda looked around the almost-empty Council chamber, and his ears drooped sadly. “Master Obi-Wan, not victory,” he said softly. “Only begun, this Clone War has.”
The words rang in Obi-Wan’s head. He closed his eyes, remembering the endless lines of clone troopers on Kamino. They were on Coruscant now — tens of thousands of clones, boarding Republic Assault Ships that would take them to fight on the Separatist worlds. There were many times as many troopers as there were Jedi, and the Kaminoans had a million more on the way. It takes more beings to fight a war than it does to keep the peace, Obi-Wan thought gloomily, and realized that Yoda was right. The war had only begun.
So there are two parts to your question. Other answers have given a plethora of sources and interesting background detail, but I think I'll just directly answer the two facets of the question.
Clone War instead of something else?As for why it was known to Yoda to be the beginning of a war, others have pointed out with great detail that tensions had been brewing for decades, and faults had already emerged. Kenobi's transmission back to Coruscant is particularly enlightening for the Jedi Council, as it confirms the lines have been drawn for a full-scale conflict, rather than just tense relations leading to outbreaks of violence in a scattered manner.
Regarding the use of Clone as an adjective for the war, there are several possibilities for this. Importantly, Kenobi seems very uncomfortable with the concept of a clone army throughout the movie. To me, it seems clear that there is a stigma to clones in the Republic, just as we have qualms about clones today. Some of this could be attributed to the Jedi's view that the Republic should not militarize itself, but I feel some is due to a prejudice specifically regarding clones. Regardless of clone's stigma (or lack thereof) it is clear that a clone army was not the norm historically, or at that time. That makes clones perhaps the most notable feature of this war, rather than the two sides.
Sorry, but I have to say it was just a sloppy bit of writing trying to get some continuity. In "A New Hope" they mention "The Clone Wars," and so there needed to be a connection somewhere.
