Quick answer: Set the TileSet to the correct Hexagon shape and matching Tile Layout/Offset Axis, then use the offset (stacked) coordinate scheme consistently when converting world points to cells.
On a hex map, tiles you place by code appear one row off or zig-zagged. The hex layout settings and your coordinate math disagree.
How to fix it
1. Set the hex shape and layout
In the TileSet set Tile Shape to Hexagon and pick the Tile Layout (stacked or offset) and Tile Offset Axis that match your art's orientation.
2. Use the editor's coordinate conversion
Convert positions with local_to_map and map_to_local rather than computing hex offsets by hand, so staggered rows are handled by Godot.
3. Keep one consistent convention
Pick offset (stacked) coordinates and use them everywhere; mixing axial and offset math is the usual cause of a one-row shift on hex grids.
Catching the ones you can't reproduce
The hardest version of this to fix is the one you can't reproduce — it only happens on a player's hardware, OS, driver, or save state, under conditions that simply aren't present on your machine. A report that says “it crashed” or “it froze” gives you nothing to act on, so the bug survives release after release while quietly costing you players.
Automatic error capture closes that gap. Each failure arrives with its full stack trace, the device and OS, the build number, and a breadcrumb trail of what the player did right before it broke, so even a failure you have never seen becomes a specific, reproducible issue. Fold identical failures into one signature ranked by how many players each hits, and your worklist sorts itself worst-first instead of arriving as a stream of vague complaints.
This is where a tool like Bugnet earns its place. Its SDK captures every Godot error automatically with the full stack trace plus device, OS, memory, build, and game-state context, folds duplicates into one grouped issue with an occurrence count, and ties each to the build it first appeared on — so you fix the problem that hurts the most players first and confirm it is gone when its signature disappears from the next release.
A crash you can name from its stack trace is a crash you can usually fix in minutes.