Because sometimes Tomcat is taking more than three seconds to shut down.  It
tries to shutdown all of the applications it's running cleanly, and that can
take an indeterminate amount of time (well, there is an upper bound before
it just kills them outright, but it's large.)

One more reliable way to do this would be to write a Java program that tries
to bind to Tomcat's socket in a loop (not a tight loop; put a sleep in)  and
doesn't return until it can (or until it gives up after some timeout) and
have your script:

stop Tomcat
run bind-to-socket program
wait N seconds to be sure it's down
start