SpaceChem has bitrotted a bit. It uses SDL_image 1.2.12, a version that surprisingly broke on modern OS X, and it's very picky about the version of Mono required. (Must be 32-bit, must not be 4.3+ - Mono broke something. Ugh.)
But I'm here to take all your troubles away.
Patcher app: -> https://github.com/leafi/fix-spacechem-os-x/releases/tag/v2.2
Note: This is for the Steam version. I have no idea about anything for the Humble Bundle version.
The app downgrades the particular shipped version of SDL and also includes a known good standalone version of Mono (thanks to MonoKickStart). Run it, or read on for more rambling technical info.
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Without MonoKickStart: SpaceChem doesn't include Mono - you have to install it yourself - and Mono 4.3/4.4 break some web stuff so you need to use Mono 4.2 or older, and you need to make sure you use 32-bit Mono not 64-bit Mono, and...
Visit the Wiki if you want to understand what the hell is going on. It's very hairy.
Ah, this page used to be full of technical stuff. I found a thing called MonoKickStart that lets you ship Mono inside applications, and now everything is hunky dory.
bonsai.tar.bz2 is an archive with all the files to be updated/replaced in SpaceChem.app, curated and massaged by yours truly based on Mono 4.2.4.4, and fix-spacechem.sh is a script that'll copy the files over.
'Fix Spacechem.app' is just the script in .app form, running in a window. Nice little program called Platypus did that.
Everything's here, so if you don't trust me at all or you're just curious, dig through the wiki and the tarball.
Make issues on GitHub ideally, or complain in that Reddit or that Steam thread.
Try to cd into the Resources directory inside SpaceChem.app and do ./SpaceChem.bin.osx from a Terminal. Copy the output, and if it says it made a .zicrash file somewhere (and it will), please go find that file. (It's a zip file with a funny extension; if you rename it, you can see exception.txt inside which is really the key here.)