That isn't an inconsistency lol. Sheldon goes to hospitals numerous times in the series. And as he grows as a character, he also learns to cope with his nuttyness. As far as the stuff with Stephanie, Sheldon is able to put aside one crazy thing for another. So in this case, his compulsive need for testing takes over his irrational fear of hospitals and germs. He feels it's necessary to be there for the tests and that supersedes his fear of germs. Just like his fear is superseded by his love and concern for Leonard when Leonard gets surgery.
There are other inconsistencies though. But most shows have these issues, especially from later episodes ignoring early episodes. Like Howard talking about things that worked for his parents like not talking to each other and drinking. He mentions those in the first, and i believe, second seasons. However, we all know howard's dad left when howard was just a young kid (before he was a preteen if i remember correctly), so Howard wouldnt know what worked or didnt. Furthermore, those things obviously didnt work because his dad was a b**** who abandoned his family.
Penny's life's inconsistencies bother me the most. Sometimes she is from Omaha, sometimes she was raised on a farm, sometimes it seems like she was raised in the city limits, and other things like that.
Leonard's father's inconsistencies can be explained by character growth. When leonard's heartless cold mother was no longer controlling Leonard's father, he was able to show his true colors that he was a warm and caring dad and not the monster that graded christmas homework as a present and ignored Leonard for a skeleton boy lol.
Bernadette's inconsistencies do bother me. They had her voice as Melissa Rauch's voice, but then changed it to a higher pitched mousy voice. Not to mention all the inconsistencies with her family life vs what we see.
Amy's are easily attributed to character growth.
Raj is about the only one without inconsistencies, although Sheldon's family's are few and far between, and that isn't used as a trite phrase. We see some inconsistencies from very early episodes vs the last 9 seasons, but they are rare and not very prominent.