Can someone explain why the aircraft does this? What does it limit the altitude too? Does it set a minimum height or a maximum, or both. Does it happen because of wind or lack of visibility? Any insight would be appreciated.

What Phantom do you have?  In the Go App, you can manually set the maximum height/ altitude up to 500m. This is related to where you start/home point set =0

GM01 Posted at 2016-3-23 16:24
What Phantom do you have?  In the Go App, you can manually set the maximum height/ altitude up to 50 ...

I have a phantom 3 advanced. My altitude is limited to 120 meters which is where I like it to stay. Am trying to film videos at low altitude, like 3-10 meters. Sometimes it tells me "aircraft enters altitude limited mode" and then flies through the waypoints accurately but seems to make adjustments to the altitude like adding a few meters, maybe even 10 or so. Very unpredictable and annoying.

cmoriarty1 Posted at 2016-3-24 12:27
I have a phantom 3 advanced. My altitude is limited to 120 meters which is where I like it to stay ...

Not a good idea to try and fly waypoints at altitudes between 3 and 10 Metres, the altitude is set by a barometer and it can exhibit errors within that range.

sorry double post

I had the same problems when flying waypoints. I sent it in 4 times and they could not fix it so they replaced it with a refurbished Phantom. I was not happy. I do wish you luck... If you send it in just demand they contact you before they send it back and ask what was repaired... this is under warranty as long as you are within a year of purchase.

Butch