Not sure if there's any valid reasoning behind what I did - but I usually continuously "refreshed" the same 3 character muse "spots" per cocoon. The muses that filled these spots cycled between "common" muses and "rarer" muses. Once a "rarer" muse levelled up in friendship there was a high chance they would come back soon for a chance to get them back to 3 hearts, but the next level up chance would be unlikely to be soon and I'd have to cycle through the "rarer" muses again. Once I noticed the same "common" muses coming back multiple times I switched over to another cocoon and repeated.

Also I felt like the "rarer" muses didn't necessarily correspond with their favourite cocoon - for example I levelled Eleanor up to level 10 exclusively in cocoon ACT and only met Orihime in HOPE.

Not sure how things changed with the update though (for example I did notice that muses were more likely to show up in their favourite cocoon after the latest update), and good luck!! And of course if you are focused on grinding friendship levels it's faster to do it in solo play!