I’ve had a recent issue with the merging stacks option which allows you to pseudocolor two or more different stacks of images (with two or more stacks open go Image/Color/Merge channels).
If your stacks are named the same way (which happens a lot in microscopy for different channels of the same image), the way to attribute them different color is to just select them based on which one you opened first when merging. I’ve been using this feature across different OSs for the last 10 years without a problem. This still works fine for ImageJ 1.52a + Windows10, however, if you try it on ImageJ 1.52q + macOS Catalina 10.15.4 then it won’t be able to merge your channels. It’ll create a composite of however many colors you selected of the first stack (not helpful).
A way around it is to give your stack different names, then it works on ImageJ 1.52q + macOS Catalina 10.15.4, which can be used until this issue is debugged.