I'm going with you're using one of the latest apktool versions (I'm using 2. beta9)
Look for the line that errors out. Most likely it might be something like this
That 9 means the line
add a + before layout so it looks like this
<include android:id="@id/photo_update" android:visibility="gone" layout="+@layout/photo_updates_header" />
Once it compiles, grab that same xml from the untouched apk and drop it into the new compiled one. Unless of course you're using a vrtheme type of zip, then you just gotta remember to no add that xml..
Just a heads up, the clock apk has about a bazillion lines you have to do the same, but mixed in like 10 xmls....
ibotpeaches thread is where I keep in touch of what's the newest apktool
He doesn't post the newest betas in the op, so you gotta use search to find them.........(DAMMIT I GOTTA SEARCH?)