90 days to delete my data? Is a real person going to every server and manually changing the bits that store it? :) ... I wonder if this is an artificially inflated time period, just like the 'Unsubscribe' feature from unsolicited emails that tell you it might take "7 to 10 days" to unsubscribe your email address, when it should take less than a second.
Some years back working with another social service, a major issue was cached data through third-party providers (think Akamai, Limelight, Cloudflare, etc.). These are systems 1) outside the primary service's immediate control and 2) with their own data-retention policies and 3) data management tools.
Someone I knew was tasked with removing large quantities of image data that had proved inopportune. There was limited support for doing this, though a method was developed. My understanding is that the caching service provider hadn't had to deal with such matters at that scale previously, though this information is incomplete. I strongly suspect that this is more frequently encountered now.
I'm not excusing Facebook (and generally avoid doing so), but one of the interesting things about scale is, well, its sheer scale, and what seem like simple operations become complex.
Maybe they have different tiers of backup systems, and manually trying to go in there and deleting one person's data on demand can be "expensive", so they do it in batches. You're only guaranteed to be fully wiped off after a certain amount of time.