How did you create your mask?
What, exact, version number of AE are you using?
Thanks for the reply, and
It was around thirty frames. I split every frame and masked each one individually with the Pen tool. I am using After Effects CC 2015.
When you are trying to troubleshoot a comp select the layer that is giving you problems and then press the u key twice to reveal all modified properties of that layer. Make sure the CTI is over the frames that are giving you problems.
We don't know anything about your project except that you apparently split up the Beach Opening 10 MP4 video into a bunch of separate layers and then drew a mask on each one. We also know that the comp is a non standard frame rate. Unless you know exactly what you are doing this is ALWAYS a bad idea. Your comp is also 20 minutes and 4 frames long. I expect that you are trying to edit a movie in After Effects. This is also a very bad idea.
If you are trying to separate the characters from the background this is a terrible workflow. You did way more work than you needed to. You should have kept the video on one layer and then rotoscoped the footage or maybe even used RotoBrush to separate the characters from the background.
I am suspecting that you got the MP4 from a screen capture program and that you are new to AE. MP4's are highly compressed and each frame must be reconstructed from some averaged color and luminance information. The decoding process can get fouled up quite easily and I suspect that this is part of your problem. Splitting the layers up into frames (btw not all layers are the same length and they should be if the frame rate of the comp matches the frame rate of your captured footage). I'm afraid that you are going to need to do all the roto again but it shouldn't take you as long as it did the first time.
Don't split up the layer, just set the in and out point to include just the footage you are going to use in your final edit. Make sure the frame rate of the footage matches the frame rate of the comp. It would also be a good idea to render a production quality intermediate using the Adobe Media Encoder so you don't have to deal with potential problems from highly compressed MPEG files.
Give Rotobrush a try but not before you type Rotobrush in the search help field at the top right corner of AE and go through some tutorials. You will not be able to just start using the tool and have success. It's not intuitive to use and if you use it incorrectly it will not work properly.
If Rotbrush doesn't work then you will have to rotoscope by hand. There a lot of ways to do this but this tutorial should give you some of the basics. I hand roto all the time and you don't usually have to adjust the masks on every frame.
Don't try and edit in After Effects. AE is designed to work on shots that you need to apply effects to or process in ways that you cannot do in Premiere Pro or any other NLE. Single shots or on occasion short sequences are efficient workflows in AE. Cutting a 20 minute movie in an AE comp is horribly inefficient and changes are incredibly difficult. 90% of all my AE comps are 10 seconds or less and have only one shot in the timeline. Most have a bunch of layers, but I almost never try to edit a sequence in AE.
I am using After Effects CC 2015.
What exact version number? It makes a huge difference if you're on 13.5.0 vs. 13.7.2