In my experience it comes down to the over simplified fact that you don't coast on a trainer. Constant resistance.
This magnifies anything slightly off, so as suggested above, I'd cut down on time and resistance. Don't compare "trainer distance" to "road distance". Do use the trainer for intervals, on legged pedaling or a way to exercise through a web meeting. Do think of the trainer as a different type of riding.
The under patella pain is common for people riding outside when they ratchet up hills early in the season with lower cadence. Which makes me think the trainer is acting like a low grinding hill for you with the constant resistance.