Can Invisalign Make You Nauseous?

I would say Invisalign may have contributed to the situation, but likely not the cause. Similar to an ear infection affecting balance, changes in the bite can affect the TMJ on one or both sides. The effects are likely temporary, but this may be a sign of something else as well.
I suggest a consultation with an ENT to rule out other pathology.

I've only seen this happen to one patient so far. Some people may have nausea triggered by prolonged stimulation of certain areas of their mouth, especially on the inside of their lower teeth near their tongue around the first and second molar area. While the trays do not extend far enough to touch the gums, sometimes the stiumalation of the tongue can cause this sensation.