There are few things as frustrating as trying to figure out why a pet is marking indoors. The reasons can be complex, from illness to the way a pet is interacting with other animals.
But another possible trigger is household cleaners — particularly if you're using them to clean up after a pet "accident." Animals perceive scents very differently from humans. Particularly suspect: bleach, and cleaners with citrus fragrances. Try switching to natural cleaners.
If you need something with a little scent to it, pets seem to be less disturbed by floral essences, such as lavender. Of course, your vet is the best resource for advice on the safety of any cleaning agent or specific suggestions on behavior modification.