If you look in a ZenGM Baseball league export (Tools > Export League) or in the customization documentation, it's clear that ZenGM Baseball league files are fairly complicated. There are a lot of different ways that things can go wrong, and some of them can be subtle things that you don't notice immediately.
When you create a new league with a file, you may see a warning like this appear (and probably this is what brought you to this page):
This means there are some problems with your league file. Maybe some required fields are missing, or some values are in the wrong format. It might work, but it might not. Especially if you're sharing this file with others, you should probably fix the errors to be sure.
Click the arrow below "JSON Schema validation errors" to see the details for each of the two errors:
The first error means that the "tid" property of the 4th team is supposed to be an integer, but instead it is a string. You can see this in the JSON file -
"3" should be
The second error means that the 15th team is missing the required property "did", which is the division ID number. Again, you can see this in the JSON file. (See teams customization for a description of this property, and game attributes customization for more information about customizing conferences and divisions.)
If you fix both errors, then when you upload it again there will be no warning. Hopefully you can do the same thing to fix any problems you're having with custom league files.
Here is a link to the JSON Schema file, in case you want to use it in some external validation tool.
There is one big caveat here. Just because your league file passes this test, it does not guarantee it will work. This checks some (not all) structural aspects of your league file, but it does not check the logical relationship between parts of the league file. For instance, if you say a player belongs to team 28 but you only have 20 teams in your league, that is not going to work correctly, but this check will miss it. Some day there will be more comprehensive checks that include stuff like this. Baby steps!