Author here - check that the revealed ships in your puzzle are keeping their particular shape. E.g. a revealed-at-start "D" shape ship-end can't be the middle of a ship, or an "O" submarine, or face a different way that it's initially facing. 99.9% of the time people report this, it's a confusion about that aspect (if you can think of a way I can make it clearer definitely let me know!).
The simplest way would be to also pre-fill forced empty spaces. It 'solves' part of the puzzle for the player, but hopefully that wasn't a key part of the fun. You go as far as to explain all of those bits at the bottom anyway.
This kind of thing is done to great effect in "Good Sudoku", which gives players a lot of automated tools for the simplest things, as to lead players to handling the more fun, more complicated parts of the hard puzzles.
I think the easiest way to make it clearer is to highlight it in red as a mistake if done incorrectly, as you do with the counts on the row ends. If you try to place a ship token close to another one then you should also highlight it in red.
