Yes, that’s a good think to read doc an play a few with software before really using it for important things 
And don’t worry, this post will stay opened and available if you still encounter the same problem, you’re welcome 
@Loni_Dove, I think @AhabGreybeard start to talk about this subject because it seems that you’re lost at the beginning with the save functionality, and maybe there’s something to improve to Krita with this.
In GIMP, few years ago they decided (I think with release 2.8, not sure) to allow save of files only to .xcf format.
To save a file to another format, you have to explicitly do Export
For me, at the beginning, it was very boring.
For me now, it’s just boring.
Because I know what I do when I choose to save to a format or to another one.
But for newbie it could be more difficult as .kra file format is not as popular as .psd for example
But I agree with @AhabGreybeard, discussion about Save function should be made on another topic to allow to everyone to know what we are exactly talking about (here, we try to understand why you got an imprint on final result)
Grum999