I had the same problem when I started working at a startup a few years back. The code base was a spaghetti factory, but that was the least of the problems. No one was prioritizing issues properly, management was aloof, the bugs being discussed in the product were huge oversights, deadlines were looming, but nothing about the trajectory was indicating that anything would be met. I left after a week, a year later, they went out of business.
So I guess the take away is, if it's just code, being new, you will always run into differences, poor code (maybe there were reasons for quickly scrambled code), oddities, but don't let that throw you off, maybe they need more people so they don't need to scramble so hard? Bringing it up, or butting heads will only keep you from progressing. If you want to stick it out, assimilate and just prove yourself through superior code/work ethic. But if the code is a symptom of a much bigger mess in the company, then maybe look for something else? It's tough, and we would really need to be there to understand the whole situation.