Perhaps it did.
Harry never had any interaction with the Elder Wand (prior to the final battle with Voldemort). He didn’t disarm it from Dumbledore, nor did he disarm it from Malfoy. All he did was disarm Malfoy’s regular wand.
In order for Harry to have the Elder Wand’s allegiance, then, we have to assume that when one wizard disarms another he gains the allegiance of not only the wand he disarmed but all wands currently under the allegiance of that wizard. By disarming Malfoy Harry thus gained the allegiance of all of Malfoy’s wands, one of which was the Elder Wand.
Now let’s consider Ginny. If we assume that the Bat-Bogey Hex counts as defeating an opponent then that would mean that Ginny gained the allegiance of all of Malfoy’s wands at that time. Then a year later Malfoy defeated Dumbledore and acquired the allegiance of all of Dumbledore’s wands, including the Elder Wand.
Almost a year after that Harry defeated Malfoy. That means that he then acquired the allegiance of all wands whose allegiance was to Malfoy. That would include the Elder Wand but it would not include Malfoy’s original wand. Since Harry never defeated Ginny, that wand still owed its allegiance to her (or to anyone who may have defeated Ginny in the interim).
The conclusion of all this would be that Harry had the allegiance of the Elder Wand without ever interacting with it, but he did not have the allegiance of Malfoy’s wand despite disarming it from him.
It is perhaps noteworthy how Harry's relationship with Malfoy's wand is later described in Chapter Twenty-Six of Deathly Hallows:
Harry looked down at the hawthorn wand that had once belonged to Draco Malfoy. He had been surprised, but pleased, to discover that it worked for him at least as well as Hermione's had done.
This doesn't tell us that Harry had won the allegiance of Malfoy's wand. All it tells us is that Malfoy's wand worked as well for him as Hermione's wand did. Harry had not won the allegiance of Hermione's wand. The reason why Malfoy's wand worked for Harry would be that any wand can work for anyone, though various factors can affect how well they work. As Ollivander told Harry in Chapter Twenty-Five:
“Oh yes, if you are any wizard at all you will be able to channel your magic through almost any instrument. The best results, however, must always come where there is the strongest affinity between wizard and wand. These connections are complex. An initial attraction, and then a mutual quest for experience, the wand learning from the wizard, the wizard from the wand.”
Thus, Malfoy's wand worked as well as Hermione's wand because they both may have had some level of affinity with Harry, but that does not necessarily mean that they had the higher level of full allegiance. The true allegiance of Malfoy's wand may have actually been to Ginny, but the Elder Wand had never been won by Ginny.
