Can flies get in the house from the septic tank?
The flies could be getting in from the septic tank if one or more P-traps has dried out. If a P-trap that has completely dried you could check it by pushing something flexible down the drain a few feet and see if it is wet when you withdraw it.

Unfortunately a P-trap does not need to have completely dried out to in order to lose its effectiveness in blocking the drain of updraft from the septic tank. So in this case you may be better off to simply run a good bit of water down each drain in the whole house and then re-evaluate the fly problem sometime later. 

Keep in mind that flies could be entering through:


Furnace vents.
Chimney/fireplace.
Plumbing vent stacks (also related to dried out P-traps).