In the end, they decided that the existing Falcon 9 cores with minor modifications could be used as the side boosters.
The difficulty came in the center booster. This needs to handle the load of the two side boosters, and carries the heaviest load (Second stage and payload).
Additionally seperation is trickier than any they have tried to date. Currently the use a pusher to shove away the second stage. This is a totally different type of separation event. Have to make sure they fly away, not back into the center core, they have to be pushed away firmly enough, but not with something that can damage the remaining center core.
Issues with handling engine out become much more problematic. On a single core, if an engine has trouble, it gets shut down, the computer decides whether to throttle the others up, or else just run longer to compensate.
Now you have two side boosters each with 9 engines, and one engine shutting down you have to balance the thrust difference across the entire stack. That is probably a lot more complex than you would imagine. Especially with 27 engines across three cores.