First, as this was an internal Schengen flight, you should not need any documentation other than ID (and even that, not always) to board that flight. For some weird reason Ryanair go over the top on this and check anyone with a non EU/EEA passport even on internal Schengen flights, but this is actually not a legal requirement. It may even be illegal, though I don't think there's definitive word on that.
Next, the (very very long and complex — 120 pages!) list of residence permits which allow entry into and residence in the Schengen Area tells us:
GERMANY
(...)
- All other documents issued to third-country nationals having equivalent value to a residence permit
(...)
Fiktionsbescheinigung
(Provisional residence document)
Only if the third box on page 3 is ticked – the residence permit continues to be valid. Entry is allowed only in connection with an expired residence permit, visa, a valid passport pursuant to Article 10 of Directive 2004/38/EC, or a German permanent residence card pursuant to Article 20 of Directive 2004/38/EC.
If the first or second box is ticked, the “Fiktionsbescheinigung” does not entail the right of entry without a visa.
The third box is "der Aufenthaltstitel als fortbestehend (§ 81 Abs. 4 AufenthG)", which you tell us is ticked.
The agent was probably confused because the same document may or may not be valid depending on which box is ticked. I understand their plight given the very large number of documents and variations and the fact that a check in one box or another changes things, but they're just plain wrong, and should have supporting documentation (the above Annex 22 list) to make the correct decisions, and should refer to it when there is any doubt.
As you were incorrectly denied boarding, you are entitled to:
- Compensation (250 euros in this case)
- Reimbursement (refund) or rebooking at a later date.
It is a requirement that you first request this from the airline. It looks like this should happen from the "My Bookings" section of their website, but I don't know if the feature will be enabled in your case (as they certainly think you are not entitled to compensation or a refund). If you can't do it that way, you will have to use whatever contact form you can find to notify them. Alternatively, you can send them a letter (by registered mail).
If they refuse (which they will probably do), then you have to take it to a dispute resolution service and/or a national authority.
The alternative is to use the services of one of the many companies which will do all that for you, but will of course take a cut (usually 30%) of the proceeds.
Good luck!