Please upgrade Mastodon. 
https://github.com/tootsuite/mastodon
I found that QOTO does not hide those statuses from muted accounts. Although I don't know if this problem is related to the software version. 
One of my following boosted a status from a user I muted. That status still appears on my QOTO timeline while I'm sure it is hidden from my timeline of another instance, where I have almost the same following list. Clients don't matter. I've tested on both web and iOS (Toot!).
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What's interesting, when I just muted that user, their status did disappear from the timeline immediately. However, it did come back when I refreshed the homepage. lol
