This is not a bug, it's because the Sky Block XP points and level system is based in how big is your island. EVERY block has a certain value of points (More expensive blocks, give more XP points) and when you check your score the system counts all your island blocks, multiplies the block types count for it's point value, and sums the score obtained. Every 1000 XP points you get a new island level.
Also, If you do /island info you will know exactly how many blocks u have in your island and how many points you have in total, and tells you how many points gave you the total of all blocks of a certain type. Therefore, it's logical that if you mine a block from your cobblestone generator or you chop a tree, your total XP points decrease, as there are less blocks in your island. Nevertheless, you will notice that if you place the mined block again you will get your lost points back
