Dana offered him a shit ton of money, but would not budge on Fedor fighting in Sambo. Fedor's people confirmed that Dana offered a shit ton, so this is not just speculation.
Fedor wouldn't budge on not fighting Sambo, and he also didn't like some other clauses that are standard in the UFC contract, like the champions clause. he liked fighting in Japan on NYE and some other stuff too. so basically he didn't want to be "tied down" to UFC.
UFC had no interest in budging their standard contract stuff for Fedor.
so far as i can tell, both sides had demands, and stuck to them. no more, no less. if it didn't make sense for Fedor to take money and feel obliged, then by definition it didn't make sense. likewise, i can very much see why Dana wouldn't want to create a one-off contract just for Fedor.
Finkelstein didn't help any by suggesting (demanding?) that his org help in the production, or distribution in E Europe, or some such thing. what some called "co promotion", although that term got thrown around pretty loosely.
so ya, it pretty much came down to Fedor's demands were worth more to him than millions of dollars. and anyone who claims he is "wrong" has no standing; they can say THEY would have taken the $6m or whatever, but they cannot say "Fedor is wrong in believing that his beliefs are worth more than money", cuz they aren't Fedor.
hope this explanation helps. most people cannot give a straight forward, unbiased answer; they're too caught up in their "because Dana is a leech" / "because Fedor is stoopid" / "because Finkelstein is Russian Mob" / "because i'm too stupid to be reasonable" drama.