Process suddenly starts using lots of CPU

I have a java chat socket (nexusServer) running on my system. Under normal circumstances, it only uses few resources as it's just a socket passing on data to the actual IRC channel, not a full IRC application itself.

A couple of days ago, nexusServer suddenly started to go really heavily on the CPU (80-100%), and using "top" I could also see that the time running was climbing almost identical to real time (under normal use, it usually stays at 0:00 because the connection times are really short). I watched it for a bit, and after 1:30 hours finally killed the process. I waited a while, then restarted it, and again for about a minute it did the same thing (going heavy on the CPU) and then suddenly went back to normal.

I am assuming that someone was massively scanning the particular port, or that it was maybe even a DoS attack of some kind. Needless to say that I am somewhat concerned. I've only had the server for a couple of months, and although I am trying to learn, I am still far from being an expert. So is my assessment/guess correct that such a behavior can be triggered from the outside without security having been compromised? And I assume that whether or not such an event might LEAD to a security compromise basically relies on the program listening to that port (nexusServer in this case) and whether or not is has some security flaw (leading to a stack overflow or whatever) that the attacker can use to his advantage?

Or am I totally on the wrong track and what I have described can much more likely be caused by...?

Many thanks in advance!