Yes, it is very frustrating.
Really though, there are two main issues here - where are the trackables going and why isn't the cache inventory correct?
Why the trackables are missing? Who knows why people do that! I cannot fathom why cachers collect other peoples' bugs. What is the value in that? Are there some sort of geeky, rogue cachers that get their kicks off stealing trackables and showing them off to their other geeky, TB stealing friends? I guess so. Of course, you have the cachers that cache once a year when they are on vacation, yet still take bugs (these people really drive me nuts!) and really don't know how to log them. Throw in a few just plain lazy cachers and you have a mess!
If these people can read to geocache, they can read how to log a Trackable. No excuses in my book. I know some people say its actually okay to wait a long time (months?) to log a TB, but the "rules" clearly state the bug should be passed on quickly. If you can't or won't do that, fine. Don't pick up a bug.
I do however think the link for logging a TB should be more visible from the geocaching homepage. It is sort of buried.
Also, the iPhone ap allows you to discover a bug, visit a bug, but does not allow you to retrieve a bug. You have to log on to geocaching.com to log retrieve. Ridiculous. Many honest cachers click "discovered" from the ap when they take a bug. They don't realize this does not remove the bug from the cache inventory and put it in their possession. I am the CO of a TB hotel, and I've had to email several cachers to have them correct their log. All have been happy to do so and appreciated the help.
Finally, there is the issue of cache maintenance. If the cache owner is keeping up with his/her cache, they should know if a bug is there or not. Simply reading the logs from helpful geocaches will tell you that. The owner should then go into the cache and mark to bug as missing. It's easy to do and is a courtesy to the bug owner and future cachers. Of course, many cache owners stop caching and don't retire their caches -a whole other problem!