I don't care at all about the drama so hopefully this is suitably neutral - by the same token though I may have some facts wrong as I don't pay too much attention to things going outside the ring/cage.
I've seen Cruz call out Faber for "taking a percentage" in the past
Cruz has a seemingly irrational dislike for Urijah stemming back to at least their first fight in the WEC. He uses this comment to imply that Faber is not as geniune as he seems / doesn't care as much about his fighters due to the money aspect. You are correct that this is standard business practice, although usually the manager is not also a top level fighter. It is more relevant in this instance because one motivator for TJ's departure was that he would be paid by his new gym rather than the opposite.
I've heard there's drama around TJ leaving Faber? Why is that a problem?
There are strong concepts of loyalty in gyms, as a result sometimes an action that is best for the individual is seen as a betrayal of the group. This was exacerbated by Conor calling it in advance and declaring TJ a "snake in the grass". If I recall correctly TJ's departure was also rather sudden after denying that he was going to leave.
It can be a touchy subject because a fighter often doesn't contribute much financially when they are first coming up and they need to be trained etc - if they then leave once they are successful and making money the gym loses their investment. Similar to training new staff at a loss in a business only to have them quit and work for a competitor once they are trained up.
Who said what and who caused what issues?
Conor made the snake call, Urijah defended TJ prior to his departure, TJ left, Duane claimed that other TAM fighters were not championship level, Urijah gave his side of the story in an interview, both sides have hinted at things that may have happened at the gym. TJ and Cody are now going to be fighting so this stuff is a natural focus point for pre fight trash talk. Cruz has a long standing beef with the entire TAM gym.
Why is Cody involved?
He is essentially in the position that TJ was in prior to leaving TAM - their premiere up and coming talent at 135. He is quick to anger and loyal to the gym. Cody and TJ are both at the top of the same division and booked to fight each other for the belt after coaching against each other on TUF so conflict is inevitable.
What did Ludwig do? I just read the peanut butter story, and sure it sounds like hes a weird hustler.
Ludwig is a weird guy. Always has been since back in his K1 days and I don't think the head trauma has helped any. Watch the JRE podcast he is on if you want more insight into his strange mind. He joined TAM and became head coach, ended up focusing on TJ culminating in poaching him in a sense as TJ left the gym to join Duane in Colorado.
TLDR: TJ was Urijah's son until he ran away to live with Duane, Cody is Urijah's new son and now they are having a family feud. Cruz hates the whole family.