A single entry Schengen Visa may not be used to enter Croatia
- a dual or multiple entry is required
MVEP • Visa requirements overview
Third-country nationals who are holders of:
- uniform visa (C) for two or multiple entries, valid for all Schengen Area Member States;
You may be refused to board the plane in Athens to Croatia, since you do not fulfill the requirement of being allowed to return back to the Schengen area.
When entering the Schengen Area at the airport you will recieve an entry stamp
- general A-Visa (Transit) are no longered issued by Counslates
When leaving Greece, you would recieve an exit stamp, thus your single entry visa has been used and cannot be used for reentry, whereas a dual or multi-entry can.
In cases where the traveler has a Croatia Visa together with a Schengen Single entry Visa
- only 1 entry into the Schengen Area is allowed
- either entering or leaving Croatia once directly from/to a non-Schengen Country is needed
It would be wise to prepare a valid answer for the question that the Croatia Immigration may ask
- when and how will you be leaving Croatia?
Especially when you do not have a Schengen Visa that can be used.
It is very likely that when the Airline used the word transit, they indended it to be understood in the context of transfering from one flight to another and not in the context of an immigration status.