After playing the demo (which stayed an old version - so did not look at bugs here) I bought the full version
under GNU/Linux [current GOG version 33734 (47128)] to play it locCoop & SiPl with Logitech Gamepad F310.

I really enjoyed the great genre mix, the easy little games fitting to the entire story,
the relaxing atmosphere and the visible love for details.

Most annoying is that under Linux with Logitach Gamepad F310 the button labels are totally mixed up,
while controls work and are assigned well:
   A (green) - jump (or dive with LS-down)
   B (red) - back/escape
   X (blue) - normal action (fishing/navigation/enter door/plants care/interactions with NPCs)
   Y (yellow) - special action (e.g. start cooking - hot)

But nevertheless all the labels are plain wrong and even when knowing the right key one may thus
do the wrong thing ... which is really annoying.
The attached screenshot shows the label saying:
   "Y" to give - but giving is "X" actually and correctly, and
   "X" to close - which is actually and correctly "B" (red).

First we saw some white squares instead of the labels - and this is mentioned the devs
known bugs' page (we started in SiPl to look at the game - with both controllers plugged in,
but this should not cause any confursion).
I hope this general label problem will soon be addressed ...

Besides I would wish for a manual to get the possibilities and actions straight; e.g. what is to construct when
a new home should be built ... with the given selection this is not clear for me at all.
In the demo it was clrear - but with more choices and my recent update of the ship ... ;)
It may be nice if those possibilities are better explained (directly or in a manual).
I thinks such a PDF would be a very welcome free goodie to be added to the full game.

And my currently last point is that I would wish for all additions (especially the art book) are available directly on GOG.
It is not only convenient - it is also for easier payment in Europe while other platforms are just US centric.

I just mailed to Thunder Lotus Games about these problems (with a direct automatic reply of receiving it
with asking for patience) and will add any info from the Devs below in this thread when I get it.

Addendum for further clarification:

One can see the problem when looking at the screen of rebinding controls (1st screenshot).

The second screenshot shows a construct sub menu with 'select' and 'salvage' not getting correspinding button labels,
despite being invoked in a single player game with only one controller connected.
So this is a more general problem than currently described as known bug.

I hope this can be fixed soon ...

While the Support via mail was not that efficient, reach out via Discord:
   * http://discord.gg/tlg
was.

It seems there is now an option which fixes the problem - so if you see
other buttons then are actually used (i.e. showing wrong glyphs),
you may try to change that by Opening 'controller settings' via:
   o Options > Controls > Rebind
and in case of F310 being XBox Controller compatible select:
   o Input Icons: Xbox

For me it was quite strange to get an explanation of "limited in-game support
for third party controllers", as the Logitech F310 is still the most compatible
and robust controller around with (when playing Twin Stick Shooters) the best
Layout and no problems with empty batteries/accumulators (cable ;) and
no rumble confusion (not present) and just works even when playing more
than 5 hours non-stop. And it is sold from 03. Sep. 2010 till today - and still
superior given those two arguments.
See PDF document:
   * https://www.jmb-edu.de/pdfs/Logitech_F310_Sketch.pdf
about "F310 Gamepad Sketch & Usage incl. Distros, Resolutions & Age Rating".

Additionally it may get problematic when mixing different controllers ...
'one to rule all' ... :)

Thank you for this! I'm also using Logitec and had the same problem.
Totally overlooked this and feared, I'd have to deal with the wrong button prompts. (Had the same problem with Blasphemous before, gladly to a lesser extend.)

Edit: Sadly the triggers still don't work properly.
As prompts, it shows me A + LT to zoom in/out, what should be RT + LT instead. It also doesn't work. When viewing my ship, both triggers let me zoom out, but no button zooms in.
I tried around a bit, but no luck repairing it. And upon looking around a lot via google, I don't see a way to make it work. The game runs into problems with pads easily, even when using original Xbox pads. The devs also always explain how Steam Input and things like 360ce are not supported. (Steam Input is the last thing I haven't tried yet.)
For now I'm just using the mouse to zoom in/out, it's not an important feature anyway. But I've read of an ability bound to LT later in game. This could become a breaking point I fear. :/

I ran into the same problem with my Logitech F710. I uninstalled the game as a result. Rebinding doesn't help; the button icons are screwed up there, too.

Even though not optimal, you can try installing the Windows version and running through Wine. For me, this fixed my Xbox controller issue (https://www.gog.com/forum/spiritfarer/linux_xbox_one_series_xs_controller_not_detected) and the game runs perfectly without crashes.

Hope it helps!