Yep, if you use a process or technique that is covered by some patent that has already been awarded then the patent holder could come after you for infringement.
As is typical with patents, the patent claims appear to overlap in places, with both companies saying they have patents on the technique of boosting chemical pathways in yeast that produce isobutanol.
The Supreme Court did uphold a patent on a software-controlled rubber-curing machine in 1981, but its ruling emphasized that this was because the patent covered a physical machine that happened to have a software component, rather than claiming a software technique by itself.