Any reader of my writings will know that I'm a big proponent of evolutionary design. Despite my enthusiasm for this approach, no technique is perfect and I'm just as happy to report its problems as I am its successes.
I've come across this problem, although in somewhat different manifestations, in two projects so far.
Evolutionary Design expects the team to modify the design as the project proceeds; both to cope with requirements changes and to take advantage of learning. You can think of this as adding mutations to the design that react to these changes. This mutation is a good and necessary thing, but like many good things you can get too much of it.
The first project was a large project, with around a hundred developers. In this case the over-mutation occurred because different sub-teams would tackle a common problem in a different way. This might be by building different frameworks or by incorporating different external frameworks.
The second project was a moderate project of a dozen developers, but with a significant amount of rotation. As newcomers came in they would look at a previous way of tackling a problem, not understand it or find it deficient and go in a new direction. The trouble is things wouldn't complete before new people came in who found this half done solution had deficiencies... you get the picture.
In both cases the net result was multiple ways of trying to solve the same problem. Not just was the duplication of effort wasteful, it also made the software more complex than it needed to be.
I should stress that the overall design health was still pretty good, compared to other systems in the same organizations. In particular, the attention to automated testing allowed evolution to be much safer than the norm and both projects had significantly low defect rates.
At the risk of abusing MetaphoricQuestioning, you might think of this as a case where the environment hadn't killed off the weaker mutations. Ideally when a competing design appears it either dies quickly or kills off the existing design. The problem here is that neither happened. So the question becomes: how can you force inferior designs out of the system?
In both cases those I spoke to felt that there was a lack of overall design leadership. In the large project this was added through an architecture team that forged a base approach to these problems and then kept a close communication about what was being done. The second team hasn't tackled this issue so far, but it's seen as a need for some more stable design leadership. So rather than an evolutionary metaphor, you might think of it more like a breeder encouraging good traits and discouraging poor ones. (This was an inspiration for Darwin.)
Metaphors aside, I think it fundamentally comes down to following the principle "Continuous attention to technical excellence and good design enhances agility." Evolutionary design requires attention, skill, and leadership. It's just a different sort of leadership than many commonly think.