Yeah, there's definitely things that could be changed/improved. I actually really wanted to implement a time freeze 'cooldown/penalty' system but I couldn't find a good balance for it on time, so I just left it as it is.
With that said, sorry no dice, the Kronie Gears not freezing are an intentional "oh sh*t" moment you discover for yourself. I tried hard to design the levels where new enemies 'introduce' themselves without being overwhelming at first. I will admit there's probably 'better' presentation for such, but that's part of the challenge. "Git gud", as the kids say.