Salem

Some of the crafting recipes that require both flint and stone will:
1) not recognize you have stone and only use the flint (dropping all flint seems to unbug it)
2) Use flint first, no matter the order in your bag.
3) Use flint as stone (Not sure if it is a substitute, I haven't been playing long)

Flint is 'stone' so if recipes need stones, they will also accept flint. But i agree that it is annoying to select manually ingridient for some crafts.

Crafting recipes should prioritize "lower" value items, like stone > flint.

A good workaround for this is to pick up the two items you want to use and stick them right back into the pack when the computer won't differentiate properly. You'll need to close and reopen the recipe. The game uses the last items placed in inventory.

Example:

If you have two flint and two stone chips and want to make two rock maracas, pick up a flint and put it back down, pick up a stone chip and put it back down. Open the rock maracas recipe. One stone chip and one flint should be highlighted. You can now click craft all and get two maracas!

Most importantly, the crafting window should be able to let you choose which items to use for its various inputs.