If I use Alfred to search for and invoke an AppleScript file in v3, the script runs twice. For example, I have a script that opens a new Safari window. With Alfred v2, the script produced one browser window. Running the same script using Apple's Script Editor produces only one window. With Alfred v3, however I get two windows. I see this issue with my other AppleScripts as well.
Here's the "New Safari Window" script (saved as a .scpt file):
tell application "Safari"
make new document
activate
end tell
Alfred version: 3.0 [645]
OS X 10.11.5 (15F34)
Thanks for the great product! Very happy with v3 so far!