Trinity and Neo are in the big building with the bomb, killing everybody, and when the are done Neo is finishing the last guy off. The guy falls and drops his gun and it lands on the tip and the tip bends like rubber.
The bending of the tip of the gun may be a referral to the fact that some rules in the Matrix can be bent. Think about it. (Then again I could be completely wrong... they did make use of rubber guns during the filming of the matrix... oh well)