Had the same thing happen on my old ZJ. On the ZJ I had lost the switch under the hood which told the computer if the hood was open or shut. The switch was a single wire with a basic momentary button. When the hood was down it made contact with the switch giving a ground to the computer turning off the " open hood " message on the stat screen. This also satisfied the requirement of the computer to disable the alarm. To fix it, I just grounded out the wire connecting to the switch, so the ZJ just thinks the hood is always closed. Ill replace it one day maybe.
Our KK Liberty's have the same style switch on all of our doors, back hatch, rear glass and maybe even the hood. Open the drivers door and look for a plunger that is depressed when the door is shut. The switches are called "door ajar switch". There are 4 door ajar switches in total, one for each door. There is also one "Liftgate Ajar Switch" which is located in the frame for the rear hatch. If your hatch glass can open independently then you also have one "Liftgate Flip-Up Glass Ajar Switch " which will be in the frame for the glass in the rear hatch. These switches would cause you interior lights to switch on and would also cause the alarm to trip.
With the Jeep running, depress each switch with your hand and make sure it springs back properly when you let go. Hopefully this will cause the problem to reoccur. They could be sticking for any number of reasons. I would try cleaning them with a small brush and lubricating the plunger with clear silicone paste or dielectric grease. You may have to check for continuity with a multimeter or a test light, this will tell you if the switches are electrically functioning.
If the problem still persists then the FSM points us to the left multi-function switch. It is located on the steering column, just below the steering wheel. The control stalk that extends from the left side of the switch is used to select the dimmer lighting level and turn on the courtesy lamp.
The circuit then goes through the EMIC (Instrument Cluster) and lastly the TIPM (totally integrated power module) which is your under hood fuse box.
Check the simple first. Experience tells me its most likely a door ajar switch or it may even be something as small as the hatch glass not being shut all the way or even a leaf stuck in between the glass and the ajar sensor.
If you continue to have issues I would unhook the neg - battery connector at night just to save future headache. If the Jeep continually drains the battery low, eventually the battery will test bad and need to be replaced.
Let us know how everything works out and If you have more questions/need help just ask. GL
