This is The Shrunken City (1998).
From TV Guide:
"Shandar" is the name of an advanced, peace-loving metropolis under threat from reptilian space invaders called the Ood. To protect themselves, the Shandarians use the "Powerlink," an inexhaustible energy source sought by the Ood, to shrink their city down to a portable, domed orb. Thus camouflaged, Shandar voyages throughout time and space to hide in suspended animation on Earth. Twenty-six thousand years later, in Cochrane Hills, Pennsylvania, a construction crew unearths the city, which is discovered by inquistive teen George (Michael Malota) and his friend Lori (Agnes Bruckner).
Two kids. George and Lori, find the shrunken, bottled city of Shandar on a construction site, and take it home.
At the 14:37 mark in the video below, George pokes the tip of a screwdriver into a small opening on the side of the bottle, and he and Lori are suddenly shrunk down and transported inside it.
At the 16:40 mark, they find an oddly dressed old man, a Shandarite named Prime, standing in a vertically-positioned hibernation pod. When Prime emerges from the pod, he explains the backstory of the city, and the threat posed by the Ood, who're still searching for the city and the Powerlink.
At the 19:35 mark, we see a group of Ood soldiers materialise on the construction site where the kids found the city. They're approached by a human construction worker, and from his perspective, they too look like construction workers. The Ood alter their appearance more than once during the film, in keeping with their present locale.
At the 23:30 mark, Prime's equipment alerts him to the fact that the Ood are nearby, and fast approaching. He tells George and Lori to take the city to their elders, and warn them of the Ood. He also gives George an object that looks like a magnifying glass, and says that this will reveal the Ood in their true form.
After that, the kids are transported back out of the bottled city and restored to their normal size. Following Prime's instructions, they take the city to their local police department, and attempt to explain the situation to a Lieutenant Morgan, but unsurprisingly, he doesn't believe them.