Fly problem?

So yesterday night my boyfriend and I were watching a movie when he noticed there were just a bunch of flies in the house. He killed maybe 5 yesterday and today I killed about 4 and just saw at least 6 more!! We typically keep a clean house so I'm just not sure where the flies are coming from!! And we saw by our front door there were some ants and we thought they just came in through the cracks. Downstairs all of the windows are closed but there are some upstairs open which have a screen on them! Our house is 3 stories & we have a child and both work while I also attend school full time so our house does get messy, but never anything too serious. Maybe like our son will have toys over the house and some dishes in the sink, dust, but never anything too bad. So I'm just really confused on where the flies are coming from, we've never had this issue before! Any advice on what to do? Also help with keeping the ants away, that's pretty new too.