What program are you using to open the obj? Is it Blender or something else? Which part numbers specifically are you having trouble with? Making your model public would go a long way to help in diagnosing issues.

Thanks, I imported the Tony Stark minifig from Mecabricks library (minifigs -> Collectible minifigures -> Avengers Inifinity War -> Tony Stark-Hoodie) and then exported is as obj and then used https://3dviewer.net/ to view it.

Ok, I took a look and I think you're on the right track. For instance, the head is black with some graphics on it while the pants are grey with some graphic on them. The difference is that the image for the pants has a grey background and the image for the head and torso have a transparent background. The history of this is that the pants are based on an earlier part decoration scheme that baked the color of the brick into the image texture file. More recent decorated parts use a transparent background, which allowed for changing brick color in the workshop and this is what is driving your problem.

This is definitely a bug with OBJ export that affects the newer parts where the base color of the brick does not transfer to the the exported model.

In order to fix this, you can edit the image files that have transparent backgrounds. I recommend using an app that supports layers. I would personally use GIMP on a windows machine to do this. I would make the top layer your base image texture and a bottom layer that is filled with the color you want for the brick. Then merge the layers and save the new image over the old one. Your end result should be a skin-tone image with the face graphics on it. There should be no transparent part of the image. Then when you open your model with 3dviewer, you should see the proper background.

Thanks a lot for your analysis and looking into this! I'll have a look at GIMP, it seems to have MacOS version too.