Bureaucracy as a trap
The military's rules exist to protect the institution, not the people in it. Every time a character tries to use the system to help themselves, the system finds a way to turn that attempt against them. Catch-22 is the clearest version of this, but it shows up in every subplot.
The absurdity of war
Heller shows war as fundamentally irrational. Missions are assigned for career reasons, not military ones. Soldiers die because of paperwork errors. The enemy and the institution become indistinguishable as threats to Yossarian's survival.
Capitalism and war feeding each other
Milo's black-market empire grows because war creates demand and removes accountability. He bombs his own men for profit and faces no consequences because the syndicate makes money for everyone. Heller shows how economic logic can justify any atrocity.
Sanity versus conformity
The novel treats conformity to the military's expectations as a form of madness. Yossarian's refusal to accept the mission count, his faking illness, his constant complaints are all framed as the rational responses of a person who sees clearly. The characters who follow orders without question are the ones who get people killed.
Death and the loss of meaning
Characters die suddenly, randomly, and often without acknowledgment. Snowden's death is the emotional anchor, but others disappear mid-sentence. Heller uses this to show how war strips death of dignity and meaning, turning it into an administrative fact.