Just got the Marshmallow update last night and it seemed to go smoothly. However, I quickly noticed that many of my applications were missing after the upgrade -- and with no rhyme or reason to which ones were gone, for the most part. Everything I installed via the Amazon Appstore was gone, and even after deleting the Amazon app data and even restarting the phone, it still thought the apps were already installed and wouldn't let me reinstall them. I finally worked around this by logging out and back in with a different account, then installed one of the missing apps under that account. (Logging out and back in with the same account had no effect.) When I logged out of that account and back into my main account, the other missing apps seemed to suddenly appear on my phone again, even though I hadn't actually installed any except one under the other account.
Many that I had installed via the Play Store were also missing, some recently installed but some installed long ago, even some that were related (e.g. the Nova Launcher pro unlock/key app was still installed, but Nova Launcher itself was missing and had to be reinstalled). Some were games, some were utilities. My bank app was gone, but my local YMCA's app was still there. Pandora was there, but iHeartRadio was missing. In total, I had to find and reinstall a couple dozen apps, and I'm sure there are still some missing that I just haven't remembered yet. Fortunately, the app data seemed to be unaffected -- for example, a game I reinstalled still had my previous progress.
FWIW, the phone is bone stock (e.g. not rooted, etc.). Wish it was rooted, because then Titanium Backup would have saved me a lot of hassle. I'd go with a custom ROM but need wifi calling. The phone seems to be working fine after reinstalling the apps. I really didn't want to have to do a factory reset.
Anyway, just wondered if anyone else encountered this or if it was just my bad luck.