First up - you telling your DP to leave. Was he aggressive, threatening, intimidating, violent? Doesn't sound like it. Yes, I'm going to say you were unreasonable there. It's a joint tenancy, he has as much right to live there as you do. More right than your son and his boyfriend, in fact.
"I've since had messages off of him calling me soft and saying DS is spoilt."
And he could be right. I don't know if he is right or not, but from your OP, yes, he could be right. All I've got to go on is what you have written. Your son is 21, returned from uni but doesn't work "as he is struggling with his mental health and attempted suicide not to long ago." DS does not appear to be making any financial contribution to the household, only his boyfriend. A house rule is that they should be cleaning up after themselves and you say that "BF has broken it 3 times". Note, you only hold your son's boyfriend responsible for the cleaning up, not your son and his boyfriend jointly. On this last occasion, "DS told me he wanted BF to watch a film with him and told him the mess would be fine" - making your son primarily responsible for the mess.
It seems to me that "he is struggling with his mental health and attempted suicide not to long ago" is at the centre of the issue. It strikes me that you are handling your son with kid gloves because you are afraid of him attempting suicide again. Again, I cannot know the truth, but - how convinced are you of your son's mental health issues and suicide attempt? Because I don't think your partner is convinced, if he is calling him 'spoilt'.
Your son is living rent-free and jobless, with his boyfriend, and does not appear to be held responsible (by you) to follow the house rules. Are you encouraging him to find a job? I'm going to guess at 'no'. And you've just put your own relationship in jeopardy because your son asked you to not make his boyfriend leave.
Like I said, I cannot know if your son is spoilt, if he has mental health issues, if he attempted suicide. But I can see that you are walking on eggshells around your son, to the point where you will not enforce reasonable house rules with him, only with his boyfriend. You are expecting very little of him, and he's not even managing that. Any issues he has are not going to magically resolve themselves by him remaining jobless rent-free at his mum's with both his mum and boyfriend dancing attendance.
I can see why your partner "was a little unsure about them" living with you. And it wasn't about them "sharing a room", it was about the change in the household dynamics from a couple and adult child, to two couples. It shifts the balance. And your deference to what you perceive as your son's needs shifts the balance again.
As with so many situations, communication is required. You and your partner need to sit and talk through what each of you needs. Your son needs to communicate how he plans to address his mental health issues. And if there's a house rule, everyone needs to follow the damned thing! No exceptions.