First some questions:
- is this happening for this one specific level?
- Do you have an example of another level where the layout is different from the one you're currently showing where this is happening as well?
- If you have code for level transitions, could we please see that?
- Do you have a script or something that's part of "autoload" that we could take a look at?
- Do you have anything that limits how many enemies are allowed in one screen?
- Do you have some functionality to check how many enemies are supposed to appear in the screen?
I personally don't think I can answer the question you have but by answering these, maybe someone else might be able to slouth it out?