the nubs get stuck in a small box in the screen.
I have that as well, but it's not with all games for some reason. I don't play many DOS games, but one game I play relatively frequently is Lode Runner: The Legend Returns, which is affected by this.
The touchscreen offset doesn't surprise me that much (my understanding is that DOSBox uses relative positioning for mouse movement, which doesn't work well with a touch screen), but the "getting trapped in a box" thing does; for the record, this happens with a regular mouse as well, not just the nubs. I have never seen this happen with DOSBox on a PC running GNU/Linux (playing the same game that I get this problem on the Pandora). Maybe it warrants an investigation? In any case, switching out of fullscreen and then back in seems to solve it... weird.
One other thing I've noticed with that: changing the mouse sensitivity seems to change the size of the imaginary box the cursor is trapped in.
Another, more annoying, glitch that I have found is that when I click, the mouse jumps to a slightly different position. You can see it in my Pandora review on YouTube, where I mean to click the arrow which means "select a level", but the mouse jumps down and clicks the "play the first level" button instead. Again, this is with both the right nub and an actual mouse, and I have not experienced this on a regular PC. I think this definitely warrants investigation. It makes the mouse almost completely unusable in this game.
For the record, this is the version of DOSBox on the Repo (which has the frontend with it).