I am no expert on your machine, but I believe the Y limit switches are under the table on the right hand side, near the X servo motor. Probably have to take off some sheet metal covers to get to them.
Unexpected limit switch, perhaps there's a glob of chips that tripping the switch?
I think the switches move with the table. So, the wire to the switches could have a faulty section where it's damaged, and "looks" like the switch is tripping when it's not. The damage could be completely internal to the wire and not even visible.
I'd power up & home the machine, then with it stopped grab the cable that goes to the switch and bend & flex it while watching to see if the control shows a limit switch has operated. First, though, I'd find the switches & clear out any chips.