Sure yeah, this stuff happens all the time, and often persists until people start noticing the application being sluggish and they go and investigate and fix the slow points.

Alternatively you have tightly integrated software that only one team can work on and it takes years to come out and every time a feature needs to change its another 6 month job of reworking everything, and debugging and fixing security issues is a nightmare.

In most systems, not just computers, there's a tradeoff between a highly integrated and high performance design, vs a modularized loosely coupled one that's more adaptable and resilient.

Just look at automotives, Teslas have a unibody design that makes them cheap to build and low weight, that also makes them enormously expensive to repair and impossible to find aftermarket parts for.

Choosing maximally integrated is rarely the best path, there is always a middle ground, and one important difference between the paths is that it's usually easier to go from modular to integrated than vice versa.