Yes, please give a little more information!
Some applications do override the definitions in the active keyboard layout, built-in or custom.
This is not necessarily bad: In Photoshop, single letters work as commands when no text field is being edited – which is most of the time.
But yes, it can be annoying, e.g. the 2011 edition of MS Word for Mac changed the output for Option + any of the keys on the top row.
Fortunately, they took that out again in the 2016 edition.
So it may well be that nothing can be done and you just have to pick a different keystroke for some of the characters you need, if you want your layout to work the same in all applications.