The challenge banner (the pinned ⚠ CHALLENGE · NAME · timer · progress · ABANDON strip at the top of the factory view) was doing a full DOM replacement on every single render frame, about 15 times per second. Every one of those replacements destroyed and recreated the ABANDON button. If your cursor happened to be anywhere over the banner, the browser was re-evaluating cursor state 15 times a second, hence the hand/arrow flicker.
The "getting faster the more challenges I did" is interesting. My best guess is that the flicker itself was constant (15 Hz the whole time), but you noticed it more as you did more runs because the banner content was updating more visibly (schematic counter climbing faster, timer ticking, etc.). Or simply because once you see it, you can't unsee it. Either way, the underlying cause was always there.
Just pushed v0.9.6 with the fix. The banner now builds its DOM exactly once per challenge session and per-frame only mutates the text inside it. Button stays put, cursor stays put.
This bug dated back to v0.6.0 when the banner was first added, so thanks for being the first person to flag it. Live updates often hide this kind of thing from players because it doesn't feel like a bug, it just feels like the game is "janky" or "their computer's being weird." Much easier to fix once someone actually names the symptom.