I agree that the plant looks like it wants a bit more light. Also, somewhat yellowed leaf with the brown tip in the 3rd picture looks indicative of drought shock -- i.e. it got dried out at one point -- mint does prefer not to dry out. What looks like mummified leaf in th 2nd picture concerns me though. Is it covered with white fungus? It could be powdery mildew.
Also, you mentioned small flies? Are they tiny and have pointed abdomen? I'm thinking fungus gnats. One way to tell is to take a yellow or white piece of plastic, either cut a spike or attach it to a spike/stick/chopstick so the plastic is just above the foliage or sticking out to the side next to the soil level and smear it with petrolium jelly. Fungus gnats will stick to it. Another way is to unpot your plant and examine the soil. You'll see tiny squirmy maggots. They suck the roots, so you want to get rid of them. I usually do one of three things -- flood the soil with soapy water, sprinkle the soil with Food grade or horticultural Diatomaceous Earth powder, OR use Bt for Fungus Gnats when I have it. If you flood with soapy water you'll want to use coconut oil, vegetable glycerin or other soap without any chemical additives or fragrances. Don't make the solution too strong, though I've used thoroughly bubbly, soapy water which seems to kill the adults instantly in the bubbles -- in which case, I follow with plain water to rinse out the excess soap, which I believe can have drying effects on the plant and burn it.
If you decide to unpot your plant, check to see if the pot is full of roots or if the roots are mushy and decaying. If either, as long as you have the plant out of the pot, trim off about 1/4 of the decaying or healthy pot-bound roots and put some fresh potting soil, preferably containing compost, in the bottom and around the roots when re-potting. You could also try mixing in some used coffee grounds, tea leaves, or ground up seaweed. In the ground, mint hardly needs fertilizing, in fact, they're supposed to lose flavor if you do so go easy with the fertilizer, whatever you use, but try to use an organic fertilizer since you're presumably growing this mint for culinary purpose.
Your trap may also reveal whiteflies, which often results in progressively yellowing leaves in houseplants. They are also easily discovered by gently stroking the tops of your plant with your hand -- whiteflies will immediately fly around and then settle back down. You can CAREFULLY
vacuum up the ones that fly up. I also like using plain or slightly warm weak soapy water shower for this one -- cover the soil with foil or plastic wrap so it doen't all fall out, lay the pot on the side and thoroughly drench.
If that mummified leaf is due to powdery mildew (I don't really see evidence of it in the whole-plant photo) you might try the 1 part skim milk:10 part water spray.
Mostly, try to give your plant more light -- even moving it a few inches closer to the window or raising the pot a few inches will help -- which way does the window face anyway? North, East, West, South? Do you have a desk lamp you can shine on it? Setting the pot on white surface, aluminum foil, or a mirror helps too. You can harvest the top 1/3 to 1/2 of the mint so it'll get bushier. (You don't have to do this all at once.)
That's all I can think of at the moment.