We see the exact same problem. Note that this problem is not new. MonoGame always had this problem when using NVTT. When building large content projects with a lot of DXT compressed textures, the NVTT compressor fails randomly. It is basically impossible to build large content projects in one go. The build process has to be repeated until all DXT textures are processed and NVTT no longer fails.
I haven’t found a way to deterministically reproduce the problem. The problem appears non-deterministic, which makes it hard to debug. (Perhaps some uninitialized memory causes random errors?)
This problem was removed by using PVRTexLib instead of NVTT. But now that NVTT is back, the problem has resurfaced.