
i think it was ML's brother- Sejin heat starts while Ido is away and Ido comes back and feeling how his brother's pheromones are there, he thinks Sejin slept w his brother to try and produce an heir since up to that point Ido and Sejin never slept together. Ido then starts to assault Sejin from that point onward. (This is from what I can remember, might not be accurate)

In the novel
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Yes, the ML does rape him.
This was after he forced MC to give him a bj:
"I felt like I had a disability in my thinking. Even though I knew that what he did to me was violence, I still wanted confirmation of the reason for my existence."
These were after he raped him:
"It was Kwon I-do who forcibly brought me to sleep, even though I was intoxicated with sleeping pills. Just like Kwon Yi-jeong, he raped me, and unlike him, instead of leaving me, he picked me up."
"I was raped by two alphas and they all notified me. Since it only happened within 3 days, there was no way I could tell who the other person was."

this is a major spoiler to you and fellow readers from manhwa only
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he raped him but this is due to misunderstanding
seonho group (ido's group) planned to make henshin group (sejin's dad) to be under their wings since sejins's adopted dad offered first, in exchange to gave their omega back then, this caused ido to mad since the "omega" he think is also after power and money just like the adopted dad, the family acceptthe terms, thus sejin married, but the thing is, our sejin never defended himself, but it's undesrtandable since the life in 1st phase is a living hell, the only different from the 1st is in 2nd ido already knew his circumstances, thus sejin got stronger and can think of himself that way
about ido being a jerk is also because he is sussy for sejin since he is still working in his old company, also he still goes to his old family which is not good in ido, ido thinks that sejin will betray him one day ( it happened later in next chapter), ido was mad and his favor to sejin plummeted to the ground since this
the bad thing that'll happened is ido's brother, he's being a jerk in all timelines, he even raped sejin, thinking ido is tired of the pet, sejin who is already in bad shape after SA met ido who believed that sejin invited himself to his brother, he rapes him and since he connected via bounding he then showed all of sejin's memories, included all the misunderstanding
at this time ido felt guity, but he knew just apologies won't make things better since he's the trigger to sejin's, he even let sejin to calm himself (I personally think this is ido's fault, he should try to mend things a little by little to sejin but we know ido is not good at talking, even in second life he also can't communicated well), bad thing that happened, sejin is pregnant, but he didn't know who is the dad, in his lowest sanity, he remembered the gun, the shot himself, ido rans to him and seeing sejin died he can't forgive himself and did the same, killing himself
I'm not defending ido but I think you shouldn't gave up on this story, even in his second life, he never dared to ask for sejins's love, in chapter 73-74, if sejin goes, ido even planned to kill himself in that study, he purposely let sejin go and prepared some subsidiary for sejin at his will, he's not good at communication, but he love sejin in his 1st and second, but the misunderstanding in 1st can't be avoided, that's why he took all things to keep sejin from his family in 2nd life, he even knew minjae love sejin, but he think they're incest in 1st life ( ̄へ ̄)
if he actually did rape him in past, I'm dropping this shit. fuck this.