Is it permissible to combine the names of prophets with the name of Prophet Muhammad, peace and blessings be upon him, such as "Muhammad Ibrahim" or "Muhammad Isa"?

The default rule for names is permissibility. It is permissible to use compound names as long as they do not contain a Sharia-prohibited element or an ugly meaning. There is no harm in being named "Muhammad Ibrahim" or "Muhammad Isa," but choosing a single name is better. One can be named with one of the two names and be kunya-named with the other.