You could try:
Menu > Go (press option) > Library > Preferences
remove “com.apple.dock.extra.plist” and “com.apple.dock.plist” then restart.
Or:
“defaults delete com.apple.dock” in terminal and then killall dock.
Did this help?
If not, you can try to have Onyx purge your caches to see whether this fixes it. I’ve had this issue in the past, and ended up doing a recovery install to fully fix it.
It seems to happen randomly. Some of them show that icon in the /Applications folder. Sometimes an app will switch to that icon, then switch back to its normal icon at a later point.