This happens only with YouTube, first notification appears for about 1-2 secs then getting killed and pops again. I'm using a modded version of YouTube (iYTBP, it replaces normal YouTube so there is only one YouTube app ticked in "Notification Apps"), so I thought that might be the culprit but it works fine with Pushbullet. Also after googling a bit I found some other folks at xda who had the same problem with different apps (like WhatsApp) and say that Greenify's "GCM push for greenified apps" setting causes that for some apps even though the app in question is not greenified, and that the problem is fixed after disabling that feature. But I'm still getting double notifications for YouTube after disabling that feature and even uninstalling Greenify. Also when I try to manually push with "Send Now" (in Notification Settings), it shows once. Any ideas?
Ok I updated YouTube so it overwrote the modded one but now the problem is fixed. I guess it had something to do with iYTBP, I'll now use NewPipe instead. Thanks for help anyway.