Unfortunately I don't know how to fix that either. the Easy FPS Editor CE v1.10.5 version doesn't recognize transparencies very well. here you have this link to the github. The last update uploaded, if it recognizes well the transparencies, but I don't recommend to use it if you already have a very advanced project. I just finished it and I had some problems with the scaling of enemies and the use of projectiles.
https://github.com/CG8516/DumpingGround/tree/main/EFPSE_DEVBUILDS