I would suggest to upgrade to 0.6.0 version of JanusGraph.
It's hard to understand your case from that scope of information you provided. Generally, I would suggest checking if you always close transactions. Even read queries are opening new transactions when your read from JanusGraph. If you are using Cached thread pool for your connections (default option for Tomcat for example), you may potentially open transactions and after a while the relative threads might be evicted from pool but the underlying transaction never closes automatically (only manually). Thus, the leak could potentially happen in this situation. That said, I would simply suggest to analyze your heap dumps to see what exactly happening in your situation. In this case you could potentially find the problem which causes the leak.