There's really not an awful lot of difference between the two, they have wildly different storage mechanisms but they each have their fairly similar benefits. If you want to learn something that might be a requisite skill for a job, I would also look at alternatives such as time based and column based systems like InfluxDB and the unbelievably fast and flexible ClickHouse. While they may seem like an unlikely fit for a personal bug tracker app, there's no reason not to use them. Since I got into InfluxDB people have been requesting it a lot and I'll be using ClickHouse for all large databases, probably forever. Expand your horizons beyond your competition's.

MySQL is still more popular than MongoDB if you look at Google Trends. I've also added MariaDB, which is pretty much a copy from MySQL and its features, and PostgreSQL, which is also a popular relational database.

This is a very good article for comparing MySQL to MongoDB and which one you should use: MongoDB vs MySQL: A Comparative Study on Databases.

If you just want to learn and you have the time, I would opt for using both MySQL and MongoDB. For example using MySQL for most of the site content and MongoDB for saving log messages. As you get more and more logs you start to see the benefits from MongoDB's faster document fetching.