You’re using way more than 64x64 pixels. A straightforward way to ensure compliance with the rule is to use a canvas of exactly 64x64, then no mistakes are possible.
Yours is currently 640x640:

I created the game in 64x64 pixels. If I used a 64x64 resolution as the canvas on the website, it would be too small and unplayable. In fact, as stated in the jam rules, I scaled the size up to 640x640 to make the game easier to play. But the game is created in resolution 64x64.
In fact, if you check the games that won in previous editions, they all have canvases larger than 64x64 pixel.
But if this causes a problem and I have to change it, if you can explain how to do it so I can play at normal size, that's no problem for me.
The width and height attributes to <canvas> control the size of its backing framebuffer. So they’re not the same thing as CSS width and height. Set the “Viewport dimensions” in Itch’s controls to something large, 640x640 is good there, and the <canvas> inside will be large, but its framebuffer can still be small – the browser will scale up for you.
I don’t know how to control the canvas size in Godot, but someone in the Discord could help for sure; lots of people using Godot here.
I don't know, I made the project at a resolution of 64x64, and there isn't an export setting in Godot to change the <canvas>. Then I checked the games published in previous editions, and they have the <canvas> modified. I'll look into it a bit more, but I don't think, and I hope, that it will affect for the jam.