There are a few things that might cause this:
1) A poorly designed program or script that isn't allowing adequate time between runs of commands.
do ls -lR /
The above script would still be doing the first ls -lR when it invoked the next one and then the next one might see the first 2 etc...
It is easy to solve this by simply adding a sleep statement sufficient to make it wait for completion of first command. Sometimes a simple "sleep 1" for a 1 second wait is sufficient. For something like the example I'd probably do a sleep 120 to give it 2 minutes to list all the files.
2) Similar to the above is the case where multiple users are running the same command that eats up all the same resources. For example if you had 100 users all running "top" at the same time you'd see an issue because they'd all be competing for the same information.
3) Less common: I've seen on a couple of Dell servers with PERC cards that the PERC cards are very sensitive to heat. When they heat up they might cause a file/directory to lock. From that point on all attempts to access that file/directory hang because they are trying to complete and this will increase the cpu load ad infinitum as new processes are kicked off (e.g. locate command from cron). The only solution for this is to reboot the server to clear the lock. Of course then you also have to address the heat issue to prevent recurrence.
Note that Dell doesn't admit there is any heat sensitivity to the PERC cards so my comments are based on observation. I've seen this even when the system's diagnostics don't show any heat threshold being exceeded but the PERC card has no heat sensor. The PERC is made by LSI so presumably this could be an issue in any other LSI controller based system like the Dell PowerEdge machines.