borders getting cut off after effects

The Grow Bounds effect worked for me. Put the effect before everything else and up the pixels to something like 2000px.

Your cropped screenshots cut off important information. The top screenshot does not show what layers are visible or which layers are showing the phone. If the phone is pre-composed then Collapse Transformations all the way down to the original phone will fix the problem in the comp with the blue background. 

The phone is cut off in the first comp. Is the first comp, the one with all the layers, the template? If it is and if it still works if you collapse transformations on all the nested comp layers, you should be able to remove the frame border in your Scene 5 comp.

This is normal AE behavior. You may want to read the online help and watch a bunch of tutorials. AE does not render off-canvas content. That being the case, you have to either scale the layer to fit into your 16:9 comp or change the composition size in the comp settings to accommodate your pre-comp layers.

Mylenium