It could be because he has learned the behavior so he keeps feeling the need to do so. How long have you had him at your place? have you been cleaning the spots well?

It could be lingering hormones. It could be territorial (unbonded bunny smells). If the latter, you could try desensitizing him to the scents by swapping toys, litterboxes etc. You could also try petting him to reassure him while in his own space – to help him feel more secure?? Especially if you notice him start to lift tail.

It can take up to 8 weeks for the hormones to die down in a boy. But I suspect this has sth to do with the other rabbits. A neutered rabbit can pee mark when he’s confronted with the smell of other buns. If you manage to introduce him to the other buns properly, this is likely to get better with time. But I’d wait a couple weeks longer before making real bonding attempts. Things like bonding mustn’t be rushed.