Not sure if it's a bug or not but it's possible to swap a gem to an empty space in the grid, might have to check that out.
I found it weird in a design sense that it's primarily a very random game but all power-up rewards in the game have a very set circumstance for appearing. Line clear only appears when you match 4, bombs when you match 5 and all the goals of course are all based on matching on specific tiles in the grid. To make the feel of the game more consistent it might be cool to add a chance for power-ups to appear randomly in some form or way. Maybe spawning at the top of the screen, revealing when you break a purple block or having a chance to appear when you match 3.
I just read about the cross-clear in the description now, you have a nice variety in power-ups although they also seem to have the same effect of clearing gems. I remember in an old match-3 game called Collapse that there was a power-up which changed gems on the board to another colour, could be interesting to explore more types of powers.