I bought Cod fish on Sunday afternoon and cooked it Tuesday night.... It was a little chewy, was that because it was bad? I bought the fish from Whole Foods, so I assume it was good quality. The recipe that I used said to cut the fish into strips and cook 2 mins per side.  I wasn't sure if that meant top and bottom or all 4 sides.  I ended up cooking for about 7 minutes flipping periodically.  It was kind of chewy when we ate it.  I've never cooked it (or eaten it that I remember) so I'm not sure if this was normal.  My husband has had it twice on trips recently and he seemed surprised by the texture although he had eaten a different variety.

So, my question is: Did I ruin it by over cooking, or did I wait too long to cook it and it was going bad anyway, or is that just how it's supposed to be?
Cod tends to be fairly firm as compared to other white fish (tilapia, etc.) though it can vary a bit in texture depending on the variety.  White fish in general will also tend to overcook fairly easily and will lose moisture quickly.

Typically recipes that specify cooking times "per side" mean top and bottom - i.e. you flip the food over rather than cooking on 4 sides.  That would mean cooking for about a total of 4 minutes which sounds right to me for cod, rather than your 7 total minutes.  That's enough of a margin to result in overcooked fish.

2 days is just about the maximum for safe storage per our generally recommended guidelines (assuming you stored it properly wrapped and refrigerated) but Whole Foods does pretty well with rotating their stock, so it's not especially likely that the fish was significantly older than that.  If you didn't notice any sliminess, offensive or fishy  odor, or other outright signs of spoilage, you are likely safe.  In any case, this sort of decline probably wouldn't cause a change in texture - you'd notice the effect more in the flavor.

Now, unfortunately, since you've already consumed the fish, you might discover for yourself whether it had gone bad, but I think that's unlikely.  The most likely culprit is that it was moderately overcooked.