Unable to select some elements in the 3D model, what could be the problem?
This could be due to bad data, First try choosing File > Compress to clear any unnecessary data in the file. Sometimes that's all it needs to resolve this type of issue(s), if that doesn't work try the following:
1- Create a new file and reference the "bad" file into the new file, copy all of the elements from the reference attachment into the active DGN file, and then detach that reference.
2 - Select all the elements in the file and apply the Key-in TFREBUILD. This may also help generate the elements and strip them of any bad data.
As a good practice always back up your files to prevent loss of data.