That happened to me the other day when I tried to FMQ some borders. It looked awful. I thought it was ruined but some starch and some steam and it was back to good. I presume they'll dissappear all together when it's washed.
I also found out from these kind people that higher thread counts in your fabric can leave larger holes and that having a needle that is dull or meant for heavier fabric can also do that.
you're all so smart