The exit code for MGCB.exe - the CLI to the MonoGame content pipeline - is the number of items that it failed to build. You can see that in the source file https://github.com/MonoGame/MonoGame/blob/develop/Tools/MGCB/Program.cs
Are you 100% sure you’re building the same .mgcb with the Pipeline Tool? It uses MGCB.exe, so it shouldn’t be the case that one method fails while the other does not.
Edit: note that the automatic content building uses MGCB directly and does not use the pipeline tool