Question Perhaps a server is already running on that port? [Error Msg]

Okay, so I previously had downloaded and ran a Minecraft server from Minecraft.net (using the minecraft_server.1.12.2.jar file) and I just tried making a craftbukkit server so that I could get plugins on my server too, and it is all set up, but this error message came up when turning the server on:
"Perhaps a server is already running on that port?" which I understand is because of my other server (which I've deleted btw) so I wanted to know if it is possible to "undo" or deny access to the start.command for my old server. Or a better way to put that: is there anyway I can reverse the "chmod a+x [drag file]" step so that there is only one server? Also, I'm using a Mac!

Another thing: the server shuts down, but when I go back on Minecraft, I'm still on my server although it stopped, and I've even left and rejoin, despite the fact that it said it stopped. I even tried fully closing out of the start command terminal page thing, and I was still able to log onto my server. For my server instead of the ip, I used localhost:25565 incase that is important!

Here is a small chunk of the coding if it helps to see:
[01:30:18 WARN]: **** FAILED TO BIND TO PORT!

[01:30:18 WARN]: The exception was: java.net.BindException: Address already in use

[01:30:18 WARN]: Perhaps a server is already running on that port?

[01:30:18 INFO]: Stopping server

>logout

Please help if you can! I very much appreciate it!!!