At Ponferrada it was actually that PFP was one of the group that bridged up to the quartet Vos-Johansson-Armitstead-Longo Borghini. ELB had Ratto and Bronzini in the group behind and can't sprint, so didn't want to work, Vos was doing minimal work, and Johansson had been away solo and had less team protection early in the race, so Armitstead berated Emma during the race when the group was closing them down, mocked her for her tendency to get 2nd place in the press afterward and left the heavy implication that PFP couldn't have won the race if others had been willing to help Lizzie. She was already showing signs of this kind of entitlement back in 2010-11 when, twice in a row, she threw a strop about the British team prioritizing Nicole Cooke in the World Championships RR. The thing with the Commonwealths (a few weeks before Ponferrada) was also that, not only had she attacked her own teammate when Pooley was off the front, but she didn't work with her (didn't even look at her as she passed), didn't thank her afterwards after Emma had spent the whole day making attacks to thin the pack, pulling back others' moves and generally slaving away for Lizzie despite it - at the time - being her career swansong, which left a bad taste in people's mouths that, even though Lizzie's move was one she was entitled to make (best spot on the course for the move) and the result justified it (England 1-2, although Pooley staying away was by no means assured at the time Lizzie went past her).
However, while in most cases Lizzie contributes to her own difficult relationships with other members of the péloton, certainly I wouldn't be surprised if there's an element of frustration on the parts of Cooke and Pooley about the way their achievements were basically swept aside by British Cycling and Armitstead put forward as a kind of poster girl, especially after London, to the point where a BC spokesman publicly called Armitstead's win in Richmond a "breakthrough moment for women's cycling in the UK" - remarkable given that less than seven years earlier, the UK had the reigning World AND Olympic champion, begging cap in hand for a ride after sponsors dumped her team at the 11th hour. I wouldn't blame them if so - certainly I harbour a level of bitterness about that myself, while the attempts to present her as a lovable hard-working Yorkshire lass (always lass, never woman) felt heavy-handed, forced and ran counter to my - and clearly many others' - perception of her. However, as we've learnt in the last week or so, it's certainly not an internal thing, the fact that she rubs people up the wrong way - a lot of people from a lot of different teams have expressed very negative opinions towards her that suggests it isn't just a matter of perception.
Ironically Lizzie's own relationship with British Cycling has been fairly turbulent of late regardless of this latest turn of events; she was pretty scathing about them in the wake of the Sutton fallout.