Seems like I encountered a problem, was commissioned by UAF during playthrough, then the faction got into an alliance w/ Iron shell & Hegemony. When browsing their market however I can't access their military section because of "not commissioned". Last I've heard that being in alliance remove the commission restriction, unless there's some changes that I do not know. I also do have mods like Vayra's sector and Yunru-related mods installed so I'm not sure if those do affect the game or not.
Any military submarket, or just the November/Automata ones?
If it's the regular military submarket, might be Yunru or some other mod overriding it, unless UAF is doing something hidden. See if you can access the Hegemony military submarket while having an IS commission, or vice-versa.
Only the military submarket (In this case, I'm commissioned by UAF, and the UAF is allied with Hegemony and Iron Shell. The Hegemony/IRS military submarket is inaccessible and said that I still need to be commissioned by them), and from what I've been testing, commissioned w/Iron Shell and interacting with Hegemony military submarket, removing mods and such and still ended up with the same problem.
Also, here's my mod list for reference.
Core library mods: GraphicsLib, Lazylib, MagicLib, YunruCore
The rest: Vayra's Sector (bootleg from discord), UAF, Iron Shell, Scalartech, tahlan_shipworks, O.R.A, Kadur Remnant, Magellan Protectorate, HMI, Secrets of The Frontier, Battle music, Gundam UC, PAGSM, Sunrider, Whichmod, Industrial.Evolution, Diktat Enhancement, A New Level of Confidence (30), Starship Legends, Mayasuran Navy, DME, Progressive S-Mods, Arma Armatura, Combat Chatter, Hyperdrive, Terraforming And Station Construction, Interstellar Imperium, Immersion Friendly Portrait Pack, SpeedUp, Nexelerin, Autosave, Yunru mods(Hullmods, Low Tech/High-Tech/Midline and Civilian Expansion), Seeker_UC, Console Commands, Diable Avionics, SCY, Commissioned Crews, Audio plus.