They do say that the gem-monsters used to be actual Gems who were corrupted or damaged or whateves.

It's probably an attention to detail kind of thing, or the monster comes back into play later on.

I think, rather than damaged, they might have…birth defects.

1. Rose can just straight up heal damaged gems, yet this same episode said she couldn't find a way to help them. This could imply that it is something in their very nature, and not something you could just revert.

2. The whole nefarious nature of the kindergarten. Besides the whole 'death to all life on earth thing', there was implications that that method of making gems was 'wrong' (pearl's words when Amethyst ran away from home). If this was the way that all gems are born, you would think she would not feel as bad about it (sure, it would be wrong to turn earth into an incubator, but there must be other less populated worlds to do all this on)

3. the fact that Amethyst feels that she is 'different', and 'bad'. Undertones of that she gets from the other gems when they talk about how she was born.

4. Jasper's reaction to Amethyst. She called her an 'overcooked runt'. This implies that she could recognize something was wrong with Amethyst, and that it lead to 'quality issues'.

Putting all this together, the majority of the Gem monsters are likely gems that 'came out wrong' because of the large scale mass production of Gems used on earth.