Hey Kiryhnn,
The first energy tank in the jungle area is actually the 4th in order in the demo, sounds like you did a sequence break to use the elevator to get to the jungle area earlier.
As for losing your morph mode and missiles, there's no bugs or mechanics in the game that disable them, you likely just hit the debug keys by accident. On the keyboard number row, you can press '1' to toggle the the missile ability on and off, enabling it this way maxes out the capacity to 255, if you press '2' on the keyboard, it toggles the morph mode ability. You can open the README.txt file included in the demo zip to view the rest of the debug commands.
Other than that I hope you're enjoying the demo, playing with a controller is highly recommended. You can rebind input for both keyboard and gamepad to your liking if you don't prefer the default control scheme.
There will be an update next month near the end of April with some level design changes, proper audio sound effects, and the actual name of the game. I hope you like it enough to check it out again then.
Feel free to post any other feedback you have with the demo!