Then why was it that when the Russian Federation asked to join NATO back in the 90’s they were refused?

Do you have a source for this? I can’t find any reference apart from a random interview given by Putin.

What about when the Soviet Union asked to join back in like '48 was it denied?

It was in '54. It’s hard to know why it was rejected since all those conversations are classified, but publically it was stated that Russia’s lack of democracy was the cause. I’m sure US hatred of communism had an influence.

Though I’m not sure that USSR had honest intentions of being a long term member instead of using it as opportunity to sabotage the treaty that would be negative for their interests in the works at the time.