The ship was probably cobbled together from surplus parts made for other ships and perhaps didn't have the same fit and integration as the others did. (There's some precedent for this in historical shipbuilding, for example, the HMS Blonde was a 38-gun ship built from timber frames constructed for a 36-gun Euryalus class frigate)
Some of the secondary sources like the TNG:TM suggest that there are things as "fit" of components, such as in the fact that the Enterprise and Yamato swapped phaser arrays on the nacelle pylons because they fit better on each the other ship. In which case the Enterprise-A might have suffered from that sort of neglect if assembled from various components meant for different ships.
Or possibly the Whale Probe stuff had messed up her computer when it was undergoing final tweaks.
Some of the secondary sources like the TNG:TM suggest that there are things as "fit" of components, such as in the fact that the Enterprise and Yamato swapped phaser arrays on the nacelle pylons because they fit better on each the other ship. In which case the Enterprise-A might have suffered from that sort of neglect if assembled from various components meant for different ships.
Or possibly the Whale Probe stuff had messed up her computer when it was undergoing final tweaks.