All three of your possibilities imply that it was on purpose and understood to be wrong to begin with. What about if you made a mistake: you thought you were doing the right thing, but turns out it was the wrong thing. Or you thought what you are doing wouldn’t impact anybody negatively. Or you did the right thing but it didn’t work out the way you anticipated. Or it was an innocent and honest thing you did, but somebody else took offence anyway. You can be sorry for things without there being any malice at play.

We (humans) are not always good at predicting the future or other people’s reactions. We do stupid things and make stupid mistakes all the time and when these things affect others we often feel sorry that we did those things.