Permesso expired but I have schengen Visa! strange situation

Hello,

I am a resident of Milan, but I am currently in Spain doing my internship period which is supposed to end around mid July.
Since I am non-EU citizen, I went in February to get a Spanish Visa type D so I can enter Spain and do research activities. I was granted a Multiple entry Spanish visa for 6 months, it ends in August 2018.

I had at that time the permesso di soggiorno, and it valid until June 20. I had also visited Milan in April so I can apply for the renewal and I also have with me now the recivuta.

All the times when I entered Spain my passport was not stamped, since I was coming from Italy to  Spain.

Now, I am traveling to Romania to attend a conference for 5 days. With my multiple entry long-term Schengen Visa it seems that I can enter Romania.

But, I never had my passport stamped when entering Spain previously, and now it should be stamped when leaving Spain to Romania, and as well when leaving Romania and coming back to Spain.

Will I be asked about this?  Is this an issue? Or should I explain that I had a valid Italian permit of stay and that I entered Spain through Italy and that is why it was never stamped. 

Thank you in advance for helping me.
-Omran