Each individual blue flower can only be picked once. There should be a little sparkle animation overtop of any flower that hasn't been picked. It's not the easiest to show in a picture but if you look closely below the top blue flower has no sparkle, and the bottom blue flower does, so you can pick the bottom one but not the top one. There are 17 flowers in total, so maybe you're just missing one or two. How many flowers do you have?
As for music, none of the game files are encrypted, so you can just go into the game folder -> audio -> bgm and play any of the files in there to see what song it is. There's no way to have the game tell you exactly which one it is though. However, in some of the earlier areas the base bgm has it's pitch adjusted. The Elven Village theme is just the default Theme2 for RPG Maker, but set at 80% pitch. You'd have to adjust pitch to listen to it the same way outside of the game. If you want me to check any other music, you can just let me know what map it is on, and I can easily check it. (Or what enemy you are fighting if it's a battle theme.)
In the church there are a number of secret entrances where it looks like a wall but you can walk through it. All of the intended instances of this will have some sort of hint indicating it. Mostly, it's little glowing footprints on the ground that seem to lead straight into a wall. Ghost mode is not intended and is caused by some sort of bug. The debug menu option "Fix phasing through walls" will correct this. If you remember where you encountered this specific bug, let me know and I can try and fix it. Thanks.