When heading to Vermont Kirk and La'an see a weather report that says southern Quebec and Vermont are experiencing record high temperatures with the forecast calling for a high of 15 °C (59 °F) and a low of 8 °C (46 °F). Yet when traveling to Vermont it is snowing, those temperatures are way too warm for snow, even the low temp is five degrees above the minimum temperature needed for snow.
Finding a cold fusion reactor in Toronto with a Tritium watch from the 1990s would not work. Tritium is detected via the beta particles (electrons) it emits, which can't even penetrate a centimeter of plastic or a single sheet of tinfoil.
The painting in Pelia's possession is The Concert by Johannes Vermeer (1665-66). However, this painting was not stolen from the Louvre. It was stolen from the Isabella Stewart Gardner Museum in Boston, Massachusetts, in 1990.
Noonien-Singh and Kirk are shown arriving in Vermont, however they wouldn't have been able to cross over the border from Canada because neither one had ID.
This is explained when they are first talking to Pelia and Noonien-Singh clearly states they had to bribe a border guard.
Noonien-Singh and Kirk comment on a sunset on Harbourfront in Toronto, but they looking are southeast. So technically it was a sunrise.
If the Vulcans of the altered timeline have little to no contact with humans, how does Spock exist?
La'an and Kirk assume from the available data that she has come back in time, but it would be equally likely she was pushed into an alternate universe.
In the car, while having a conversation about names, Kirk says "Sam is his middle name. Most people call him George", clearly using present tense. Earlier, it is explained that Sam is already dead in his universe.