I believe the latest major example was at the Congress in 2010 where the ISU Council (and Mr. Cinquanta) were pushing for major changes to the ISU Constitution that would have directed additional power to the Council and President versus the Congress. These changes were defeated.
Another was at the Congress in 2012 where the renewal of qualifying rounds at ISU Championship events was set for renewal and backed by the Council. Some of the countries did not like the qualifying rounds and voted against them. No more qualifying rounds. However it backfired on many of these federations as contracts with the Organizers of the Canadian and Japan Championships were already in place that limited the expenses (room and board) that the organizers had to pay for the competitors to those qualifying for the short program. With no qualifying rounds this would have increased the numbers the organizers were responsible for by almost twice. This would have been a breach of contract. The solution that was put in place to meet the contract requirements was the "minimum qualifing score". So the minimum score was not something promoted by the Council, but rather a reaction to a defeated proposal that had contractural implications.
So it is possible to get changes made...it just takes a 2/3 vote (or over 1/3 against) on all of the issues to do so. Next week should be interesting.