The skill panel is only designed with up to 3-digit lemming counts (/ 2-digit minutes in the time limit) in mind. More lemmings can exist as long as those beyond 999 are all zombies, but yeah, it isn't designed to handle more than that.

I'd be interested to know what kind of non-troll level would benefit (ie: not just "has it for the sake of it") from having more than 999 lemmings. If such a level can be demonstrated, I'll consider doing something to resolve this issue.

For performance reasons on systems without great single core performance, I wonder if it might be a good idea to outright forbid >= 1000 lemmings. There probably aren't enough levels that use that many for content breaking to be a concern.