I'm running Ubuntu 18.04.
I've installed Krita and VLC via the Ubuntu Software store (among other apps). I have enabled multiple repositories as sources for the store.
Krita and VLC are both listed twice in my Dash: once with the appropriate icon from my current theme (Numix), and once with the app's default icon. I'll use Krita as an example for the rest of this post:
No matter which icon I click, the app launches as expected. However, I see different things if I right-click each icon and click "Show Details". If I do this for the Krita icon that matches my system theme, it takes me to a listing for Krita in the software store, sourced from ubuntu-bionic-universe. If I do this on the default-icon version, it searches the store for krita_krita and takes me to a version sourced from Snap Store.
I've looked through my /usr/share/applications folder and reviewed all the entries for Krita in there. There appear to be no duplicates, and only one (org.kde.krita.desktop) that does not have the NoDisplay flag set to true. I also checked out ./local/share/applications to see if there were any entries in there, but that directory contains 0 items.
I've tried uninstalling and reinstalling Krita, to no effect. I also tried rebooting the computer, which also did nothing.
Could having multiple repositories enabled be causing these duplicate listings in my Dash? And how can I remove those extraneous listings?

snap list, then removed the snaps withsnap remove. The duplicate entries are gone from my Dash. – SpencerDub Jul 12 '19 at 15:52