Some of it is PR: some parts have gone badly (redevelopment of Whitechapel station comes to mind), but by and large it has gone to plan (albeit using almost all of its risk time, AFAIK!). They've by and large kept their cards quite close to their chests about things going wrong, though.
The worst parts, by and large, have been around the existing railway infrastructure: dealing with long-disused parts of railway infrastructure (partly buried and exact design and current state unknown) and with currently used infrastructure without long-closures (as well as Whitechapel, the electrification of the GWML out to Reading comes to my mind, with all its problems, which is really a separate project but Crossrail cannot run beyond Heathrow Junction without it complete).
