Raising a well balanced dog you need to teach puppy how to be alone. If you don't they may well start with separation anxiety.
If she was fine in the crate before...just start putting her in the crate again for short times and build the time up. You really should give them some sort of command or say something when you leave...so that they do know that you will be back. You can say "I'll be back later"...or what I always say to my dogs when leaving is "take care of the house".
Give puppy a treat and a special toy...and leave her crated. Try crating her even if you are home, but you are busy vacuming or taking a shower,etc.
Gina