TPM does acquire software patches, and once acquired it installs MS patches just like a OS patches in most of the cases.
After running the Patch Acquisition step in the Patch Management scenario (Large environment or WSUS with SDI) on TPM the MS patches are missing despite of the fact that you can select this kind of patches.
TPM doesn't support software patches as part of TPM patch management solution.
Resolving the problem
This is not a problem since TPM is working as designed.