I have a combo Spigot/bukkit and sponge/forge server and would like to add MalisisDoors to the forge server but if I do the players would have to change clients to play on the other servers, is this a bug or a issue that was not thought of yet?

If they have mods on the client, they can still connect to the Spigot/Bukkit server, but the normal vanilla client cannot connect to the Forge server. If they are having issues connecting to the Spigot/Bukkit server with MalisisDoors added, have them disable the config option that overwrites the vanilla doors and trapdoors.

that setting allows me to play on all the servers, with no issues so far,Thanks

One question, since I'm new to Malisis doors does overwriting the vanilla doors and trapdoors change anything on the forge server?

Yes, it overwrites door behaviors making it non-vanilla in a sense. It doesn't need to be enabled, but it gives a better effect with MalisisDoors