If a program is installed via both Snap and Apt, there isn’t an easy way to tell which is which when trying to start it.
If you right click the icon in Gnome and “Show Details” it will take you to Ubuntu Software where you can find out. However the sorting in Gnome Activities search can change over time.
Some Suggestions:
Add a small Snapcraft logo to the icon
Add a small Snapcraft logo to the name
Add -Snap to the name
Can you explain more about why you have both the snap and the apt package installed?
It seems that he’s installed a program like Eclipse/Java where you need to use plugins which do not support the newer version (snap) and you need a plugin which needs the latest version or you want to keep Eclipse’s latest version. You know, for example, apt is providing Eclipse 3.X while snap is providing Eclipse 4.X.
I’ve seen this. After a fresh install I had BOTH versions of the gnome calculator application, one from the Snap store, and one from the repository. This is with 18.04LTS
The easiest way I can think of is to right click the app and select “Show details”.
Here you can always find the source
Except, when I right click something I know is a snap, this happens 
Should I file a bug for this?
Yeah, you should… Really strange