well did you came to Ireland without a valid visa? because this is a problem you shouldn't have cross the boarder with out a valid visa !!
when you sent your application what did you write in the Eu1 form on section of status on arrival in state? (because if you lied on the form then the entitlement can be revoked and in my view should be revoked)
i can suggest following
if tomorrow again your told that they cannot give you residence card i suggest you ask following
1) Application was submitted to the eu treaty right department they process the application they had a full copy of my passport they were aware of all the facts and grant me the residence card under the authority of justice minister on what ground are you stopping me from getting what is rightfully my entitlement now.
2) please give me in writing that you are not granting me residence card that is approved by the minister and state your reason as to why,
given the fact that i have provided you with my own and my spouse identification and we are both present here as per the letter which is the only instruction i was given in the approval letter.
3) tonight print the directive ( the regulation ) and read them
http://www.irishstatutebook.ie/eli/2015 ... ade/en/pdf
from INIS website and give it to the immigration officer and ask him where does it say that my previous immigration history or my current immigration status should be consider at the point of issuing residence card which is already approved by the minister.
all above is only my opinion so maybe wait for senior members to advise you
also get a solicitor to help you in this
thanks