I'll admit it - I have a love/hate relationship with MS Project. It's a powerful tool, no doubt - and something of an industry standard. And everytime I get frustrated with it, I always find myself trying to create a three-dimensional spreadsheet that would replicate what MSP does (track tasks, durations, work effort, dependencies, etc.). And my clients expect me to produce a project plan (which they hardly ever look at), so I gotta do it.
The challenge is that MSP is very complicated to use, and if you aren't aware of each setting (including the default settings for new tasks), you can do some serious damage to your project plan/ budget. For example the default setting for tasks is "fixed units". And if all you do is create a plan and leave it alone, you probably won't notice anything. But if you add or subtract resources to/ from a task after the initial creation AND have effort-driven scheduling turned on (another default) it will start changing things on you. The tricky part comes when you want to show people how they're booked on your project - using Resources Assignments - unless you're very careful, it will appear that you've overbooked your resources significantly. This is probably user error (mine), but my advice is to be very careful about how you setup, maintain and share information coming out of MSP.