You will have to use "dd" to remove the last record of the container file. The latest version of Kudu trunk (after 5.15) contains a --debug option to the "kudu pbc dump" tool that will tell you the offset of the file you should remove from the file, if you compile it.
If you can't compile Kudu from source to obtain that tool, then an easy option is to reformat the affected tablet server and start from scratch on that server, if you have additional replicas.
Another option is to use a hex editor to figure out the offset where there are is a run of 0s at the end of the file and truncate the 0s off of the file. Make sure to make a backup copy of the container metadata file first.
This will be prevented in a future release.