FLR(M) Passport not Stamped

Hi all

Came across a thread that advised people not to use the Dublin route to enter UK the very first time as the passport does not get stamped due to arriving passengers not having to pass through immigration on their arrival in the UK. Straight after reading the thread alarm bells started ringing in my head. I checked wife's passport and there was no stamp on her visa or anywhere else in her passport.

Wife landed at Heathrow on a spouse visa from Pakistan in January 2015 and I was with her at the time. It was a direct flight from Pakistan. I am British passport holder whereas she holds a Pakistani passport. Upon arrival we chose to use the British/EU passport holders queue. The immigration officer checked my passport and handed it back to me and then he looked at wife's passport, scanned her fingers and punched in some details into the system. Gave the passport back to her and let us through. I can't remember if he took her landing card from us. He certainly did not stamp her passport.

Since she came here she hasn't been abroad. Luckily I managed to find her boarding pass. Her passport has an exit stamp from Pakistan dated January 2015 but no entry stamp. We are going to apply for an extension in about 4 weeks' time. I have the following questions if someone can provide a bit of guidance please:

The fact that her passport wasn't stamped, is it likely to cause us major issues?

Is it better to book a premium appointment and explain the whole thing along with the boarding pass?

Suppose she gets an extension, is it like to cause us issues at the time of ILR?

Any help regarding this matter will be highly appreciated.

Thanks