Yeah the alpha simply bailing on the pack on the first sign of trouble would be weird even if he doesn't hold the alpha position anymore which leaves us with the possibility that it's another white werewolf or werebeast, it could also just be the alpha trying to drag Logan's attention to the pack somehow.
And it certainly could be Ruben since I have trust issues and unless people plainly declare what their intentions are, I cannot fully trust them, tho it brings me to question what he would gain from creating a new breed of swamp creature maybe going with the mad scientist vibe me and Toothless got going with our theories regarding him, he could be collecting data on how different creatures react to having their biologies drastically changed or maybe he's trying to create super soldiers or just hybrids for the secret organisation that he is probably part of.
If it's the witch and not some other power, then she could not be cashing in the favours because she doesn't really need help with what she's doing or she's just hording them for when she knows that she'll really need them like on a dramatic showdown in the future or some confrontation scene.
Circling back to the Golems I think the father is not one of them because of the vagueness we get from Ruben, sure he didn't really want to talk about the topic to begin with but he got extra vague when he got to the part about the father and just gave the need to know information, the father is important, he's guarding something, he got pissed with Ruben and expelled him from there, also if they're really guarding a gem and the father was some race not the golems them it would be easier to have something happen to him, like the golems are easily manipulated but I doubt they're easy to harm, they're covered in magic glow rocks that are super hard and they just seem inexhaustible so their endurance/constitution must be pretty high, so yea, anyway the reason that something needs to happen to the father is to expose how the golems's society is flawed and to trigger the whole live for yourself mentality, of course that would come after solving the whole debacle with whatever happens with the father and the drama that ensues.
Something completely unrelated to what was being talked above do you think that the rat king is actually a fake king of the ratkin and the real one is actually scrap? Or at least Scrap is similar to a rat king. Like this been floating in the back of my brain for a while now but Scrap and the Rat king are the only ratkin that show individuality from the rest to the point of actually having distinct personalities and interests(even if the Rat king can be debated on that account), Scrap has also shown animosity towards the Rat king that is not his usual I'm disgusted, or I'm afraid so and as for the Rat king... He really doesn't care about anything his position is more of an empty title than anything else and we don't have enough interactions with him to allow a deeper personality analysis or character flashing out, so...