Okay, so after looking at your iamges again, I noticed that it is the War Machine chest by JUICE. It says it at the top! XD So, I went ahead, tracked down the file, downloaded it myself and took a look at it.
There are quite a few overlapping pieces. At regular size, you can't tell, but once you zoom in, you see that it overlaps and even though it seems like such a small overlap, over time it can cause the build to be off. I have learned that there doesn't seem to be a whole lot of room for error when pepping as it can lead to warpage in the final pep build.
Also, those pieces that you have outline in red have another error.......want to see what I mean? Disconnect at 444, rearrange the pieces that you can clearly see the new seperated pieces. If you look closely, you will notice that on either end of the little thin piece that there are no numbers OR tabs. If you look at the bigger piece that you disconnected it from, you will also notice two "empty" places and there are no numbers. That is a result of an open edge in the model itself.
In pepakura, if you look at the model on the left, look at the red lines. These lines indicate an open edge. Most of these red lines are correct, but if you look at the red lines under the area where the arc reactor is, those shouldn't be there and it means that they do not connect to anything.
I can edit the file to make it so that there is a tab and number them so that you know where to connect it to.