
I guess what Isaac said that he was hunted by the "alpha" who knotted him, and resulted to have a son, Benjamin. That is why he labeled himself in the papers he is a beta, and did not put a residency for his son and mom to avoid being hunted
So clearly, Isaac did not know that Felix is that alpha.
Also Felix, did not also remember his past, or during is his military. But I guess will so about that.

Benjamins paternity is not a guessing game, Felix is the father and Isaac knows. Isaac even reflects back to the night they met in chapter 2, when Felix leaves the shop.
The warehouse they met in was too dark for Felix to see Isaacs face clearly. Isaac was there to kill felix so he knows for a fact Felix was the father. The artist could have reflected that better but the dialogue in spanish has Felix mentioning he wishes he could see the omegas face clearly.
I won’t spoil who Isaac is actually running from but I just wanted to clear that up.

100% !!! Spoilers ahead...
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Isaac is running from his stepfather and military commander. He technically went AWOL and abandoned his team in the mission to kill Felix (it was a lost cause anyways, they were overwhelmed and Isaac was already separated before his heat hit). His stepfather, Cole, also framed him for his biological fathers death to further corner him.
Cole wants him back because he’s a very good operative (and also a stereotypical possessive, cocky alpha). BUT thingS get more complicated when Isaac’s status as a omega, relationship with Felix, and Benjamin’s existence comes to light.
Here is a thread with more i -depth spoilers:
http://www.mangago.zone/home/mangatopic/6540163/

No worries! I thought the flashbacks made it obvious that Isaac recognized Felix and that Felix was Benjamin's father. Even the scene where Felix admitted his right hand man pointed out that Isaac recognized felix the first night in the flower shop. But it really was not clear in the manwha why Felix would not recognize Isaac back. The novel cleared up that Isaac was obscured in darkness.
I guess the story is more confusing for people because of that detail!
I was wondering why the manga is updating once a month. Manga that is so famous.
Once every two months, and it's because it's circulated on a bimonthly magazine