For your first problem, for the fish it isn't teleporting to, do you have the correct bait and do they need special weather/time?
For the fish releasing even though you have Keep all fish selected, well I have that problem sometimes too, so I think it's a bug.
I didn't use this to level up, so can't really help there, but what I can say is to add a fish that only spawns at a certain time so you will change zones and that will reset the "Fish Sense Something Amiss" message.
For adding more markers you can do this.
Go into the module folder, usually located here "C:\mmominion\Bots\FFXIVMinion\LuaMods\LedgendaryFishing"
Open the file with notepad called Location.info
You will get to something that looks like this.
Now go to where you want the marker to be and then open LUA Modules - Dev (in game with bot attached.)
Then at the very bottom on the Dev module click "Toggle Monitor Module On
Open the Player Info section and make a note of the x, y, z and h (heading) coordinates and Map ID, if you need it.
Go back to the Location.info file and create a entry, so it will look like this, entering the numbers that you got from the Playerinfo Dev console.
Save the file and reload the bot and you should be set.