You must prepare a pure culture for each one of these mixing fungi to identify them easily. Also, you must see the hyphae of these fungi, because the hyphae of Rhizopus are non septate while the hyphae of Penicillium are septate.
Also, the fungus Rhizopus produce sporangium with sporangiospres. While, the fungus Penicillium don't produce like this sporangia, but it produce verticillate phialides like hand fingers.
In the picture above, the grayish brown mycelium represents the fungus Rhizopus. While the white and greenish blue colonies represent the fungus Penicillium.
To distinguish between Rhizopus and Mucor. Rhizopus produces rhizoids and stolons, while Mucor has no rhizoids and stolons. Also the colony of Rhizopus is grayish brown, while Mucor has a grayish white to white colony.