I've started using Logic for teaching students about music production in the last two years. As I don't use Logic as my main DAW I've countered several problems with it that are easily fixed in different option menus. If you've used logic for some time and have gotten used to the defaults or you're just starting out with Logic Pro, the default settings might be completely wrong for your application. Try the following steps out to see if they fit your workflow or not.
1. The advanced tools or complete features.
I assume this default setting is for users that have upgraded to Logic Pro from Garage band. In the Logic Pro > Preferences > Advanced menu there's a list of features that are not enabled by default. These include quite basic editing functions, region colors, built in file explorer and a lot more. Enable these features to make sure you don't miss out!
2. The LCD screen at the top of Logic's arrange window
The LCD-bar contains some great information as it is such as tempo, key and signature but it can be customized further to be a lot more valuable. The LCD-bar itself has a drop down arrow menu. Chose custom in this list to get more information such as CPU load and a clock. You can even press the CPU bar to get more detailed info on the project's CPU load. If you want to customize the LCD bar further this can be done in the same menu where you can enable features like sample rate and varispeed info as well as disabling the ones you don't need.
3. The cycle bar default behavior
This one has been bugging me a lot until I found the quick fix setting. When you loop a section of audio in Logic to listen back to it a few times, the yellow cycle bar works as expected. When you want to listen to a different section however, this is not the case. If you forget to turn of the cycle function Logic will go back to it even though you're trying to play back from a different section of your song. This is very annoying but can be disabled from the right click menu of the play button. Untick the Play from cycle option in this menu and logic will only loop when the play head is in the cycle bar!
4. Region colors don't follow track colors
Coloring tracks in Logic can be a little tricky since regions and tracks are handled differently. If you're using Logic manly for music you might prefer to have tracks and regions colored the same; so that the drum regions and drum tracks have the same color for instance. This can be fixed in the preferences > display menu setting the regions to as track color. Then when you color a track using the option-c window the regions will follow.
5. The master fader
One default that can easily mess up your gain structure in Logic is the built in master fader. It sits in between you stereo track and you listening level. If you start using it to change the listening volume you may end up with some gain staging issues. For instance if I pull mine down and then forget about it i might reach a point where my listening volume isn't enough and then start mixing way louder than I should be. Personally I like to have one stereo or master track and one control for my listening level. I therefore tend to turn this feature of to not start using it accidentally. I also think this can be really confusing if you're just starting out. It can be turned off using the drop down menu from the LCD Bar once again. If you want to disable it in the mixer as well just click the VCA/Master button in the top right corner of your mixing window.