I don't know if I'd outright call it a problem, per se, since in a couple facilities (say, Fremont) it's a good thing given how good the provider (say, Hurricane Electric) is at providing transit. So in the datacenters where the provider is better at transit than facilities (say, Fremont), the equation breaks in their favor.
When I left they also didn't really have the staff to run a proper NOC for a full-on AS; one extremely talented network engineer who has since left mostly owned all the "running a grown-up network" stuff, like running down an ASN, working RTBH with the facilities, well-designed uplink strategy at Linode's edge, and lobbying for anycast infrastructure for DNS and so on. They had just hired another purebred networking wonk as I moved on who probably owns it now, and likely has help. So punting a lot of the typical NOC work upstream to a facility with whom you're already working anyway made a bit of resource-related sense at the time, since staffing a NOC for a network of that scale is a significant challenge and they like to operate lean.
That's changing now (I didn't know this and learned it from agwa's comment), which is probably reflective of growth on the resource front.