It takes a while to figure out how to read scripture. The same passage can mean something in the historical literal context, but also be an allegory to other things. The more you learn about salvation history and the more Bible knowledge you attain, you will start to see these patterns manifest. A simple story that seems straightforward to you at first may, at a second glance, bring to mind other aspects of Christian belief.
My recommendation to you is to do a few things:
I think all this will help you appreciate scripture more.
The Didache Bible is a Catholic version of the same thing I think