Yes, Muggles have harmed wizards.
In his footnote for “The Wizard and the Hopping Pot” in “The Tales of Beedle the Bard”, Albus Dumbledore stated that Muggles were indeed able to kill some wizards in their witch hunts despite wizards having the advantage of magical ability.
“1 It is true, of course, that genuine witches and wizards were reasonably adept at escaping the stake, block, and noose (see my comments about Lisette de Lapin in the commentary on “Babbitty Rabbitty and Her Cackling Stump"). However, a number of deaths did occur: Sir Nicholas de Mimsy-Porpington (a wizard at the Royal Court in his lifetime, and in his death-time, ghost of Gryffindor Tower) was stripped of his wand before being locked in a dungeon, and was unable to magic himself out of his execution; and Wizarding families were particularly prone to losing younger members, whose inability to control their own magic made them noticeable, and vulnerable, to Muggle witch-hunters.”
- The Tales of Beedle the Bard
So Muggles have indeed been known to successfully kill wizards. In fact, two of the Hogwarts ghosts, the Hufflepuff and Gryffindor house ghosts, are wizards killed by Muggles. The Fat Friar was executed because the church became suspicious of his abilities.
Hufflepuff house is haunted by the Fat Friar, who was executed because senior churchmen grew suspicious of his ability to cure the pox merely by poking peasants with a stick, and his ill-advised habit of pulling rabbits out of the communion cup.
- Hogwarts Ghosts (wizardingworld.com)
As Dumbledore mentioned in his footnote, Nearly Headless Nick was also executed by Muggles.
Gryffindor house is home to Nearly Headless Nick, who in life was Sir Nicholas de Mimsy-Porpington. Something of a snob, and a less accomplished wizard than he believed, Sir Nicholas lounged around the court of Henry VII in life, until his foolish attempt to beautify a lady-in-waiting by magic caused the unfortunate woman to sprout tusks. Sir Nicholas was stripped of his wand and inexpertly executed, leaving his head hanging off by a single flap of skin and sinew.
- Hogwarts Ghosts (wizardingworld.com)
Additionally, several wizards were executed in the Salem Witch Trials.
The famous Salem Witch Trials of 1692-93 were a tragedy for the wizarding community. Wizarding historians agree that among the so-called Puritan judges were at least two known Scourers, who were paying off feuds that had developed while in America. A number of the dead were indeed witches, though utterly innocent of the crimes for which they had been arrested.
- Seventeenth Century and Beyond (wizardingworld.com)
In addition to killing wizards, they have also injured wizards. Ariana Dumbledore was attacked by Muggle boys when she was a child.
“Aberforth glared at her: his lips moved as if he were chewing the words he was holding back. Then he burst into speech.
‘When my sister was six years old, she was attacked, set upon, by three Muggle boys. They’d seen her doing magic, spying through the back garden hedge: she was a kid, she couldn’t control it, no witch or wizard can at that age. What they saw scared them, I expect. They forced their way through the hedge, and when she couldn’t show them the trick, they got a bit carried away trying to stop the little freak doing it.”
- Harry Potter and the Deathly Hallows, Chapter 28 (The Missing Mirror)
Their attack had lasting repercussions on her as well. She refused to use magic after it so it turned inwards and drove her mad.
“Aberforth stood up, tall as Albus, and suddenly terrible in his anger and the intensity of his pain.
‘It destroyed her, what they did: she was never right again. She wouldn’t use magic, but she couldn’t get rid of it: it turned inwards and drove her mad, it exploded out of her when she couldn’t control it, and at times she was strange and dangerous. But mostly she was sweet, and scared, and harmless.”
- Harry Potter and the Deathly Hallows, Chapter 28 (The Missing Mirror)
Additionally, the fear of being persecuted could lead to young wizards turning into Obscurials.
“NEWT
I met one in Sudan three months ago. There used to be more of them but they still exist. Before wizards went underground, when we were still being hunted by Muggles, young wizards and witches sometimes tried to suppress their magic to avoid persecution. Instead of learning to harness or to control their powers, they developed what was called an Obscurus.
TINA
(off JACOB’S confusion)
It’s an unstable, uncontrollable dark force that busts out and – and attacks . . . and then vanishes . . .”
- Fantastic Beasts and Where to Find Them: The Original Screenplay
Obscurials generally did not survive past the age of ten.
“TINA
(to Newt)
Obscurials can’t survive long, can they?
NEWT
There’s no documented case of any Obscurial surviving past the age of ten. The one I met in Africa was eight when she—she was eight when she died.”
- Fantastic Beasts and Where to Find Them (The Original Screenplay)
Their deaths would have been indirectly caused by Muggles.