The short answer (with respects to problems) is everything that comes along with capital. The good news is that there is significantly less red tape to cut through for innovation!
In my journey from working at a Fortune 100 firm to starting my own company, I had a "transition" working with a medium sized company.
As I moved from the large firm to the medium company, I noticed the number of resources drop off significantly and really gained an appreciation for how much information is free when you know how to look for it. In this setting, I found that I was actually able to be more innovative as I still had access to capital for innovation experiments and there were fewer barriers as far as corporate policies.
Moving from the medium company to my own startup, the resources obviously dropped off even further, this time with respect to capital. Of course, there is no problem as far as making the go/no-go decision on pursuing an innovative effort, but I also have to be clever with what type of front end studies are performed.
Innovation as a startup is essential and it's great fun when you figure out how cheaply evaluate efforts to determine if making a larger investment is viable. Feel free to reach out to me to discuss further!