I sometimes experience something similar. When I make changes to both formation/substitution and tactics, the substitutions are delayed and I need to make one more small change on the formations and save again to have the changes applied.

What I do to avoid these kind of problems is to make the substitutions first, wait for them to take place in the match, and then change the tactics (force counter on/off etc). Or I do the tactics first, wait about 10 match minutes and then make substitutions.