I've experienced the same thing. Similarly if I put someone on hold position to defend the end of a bridge or a castle gate, they'll still abandon their position to fight an enemy back.
I think you already made the best suggestion in holding a unit or two back to plug those gaps. The main place I've run into this is in my Late era German army based around a Swiss Armoured Pike phalanx. I've got 5 units of SAP as the core of my army, and with them all neatly lined up the only flanks exposed are on the ends, well protected by swiss halbs & chiv knights, but once the fighting gets going each of the five units eventually start pointing different directions and some get pulled apart, so I keep two units of CMAA right behind them with no purpose but to protect the newly exposed flanks once the phalanx gets disrupted.
Ajax
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