Nope never had a problem like that, but I know there are many kinds of these little flies. Some or most go for dampness, & old food left around. I've seen some around my house plants, and even bought strawberry's to my Dad in the hospital that either attracted them or they came in on them.
I'd make sure humidity wasn't the problem.
Make sure the feed is not attracting them. If it sits on the floor in one spot in feed bags they could be collecting under the bag.
I have to be very careful as I buy everything in bulk. So feed has to be off the floor, hay too. Making sure air can pass all around it.
Cages need to be stripped a couple of times a year, it's amazing what collects in little crooks and crannies.
Concrete floors sweat so if things are not moved around regularly bugs will find there way in.
I am spring cleaning my chins room now so I will let you know if I find any suprises.