Didn't come up any other explanation why their programs wouldn't count for anything but I kind of doubt this would be the reason either because for example Zhuk/Britkov have also skated two Russian cup events already, and yet their programs seem to be official part of the event unlike Popova/Mozgov. Every year there have been skaters/teams who have took part more than two events. Every now and then I recall seeing that some of the skaters/team results have been deleted later but I am not really sure why this has happened. Not really sure why it happened now either. Every year there have also been junior skaters/teams who have skated more than two events but can't recall seeing that their results would have been deleted later. Now there are numerous pairs who are skating their 3rd event and their results seems to be part of the official event also.
As far as I am aware, the third event doesn't count for qualification.
Last year the same for Shevchenko-Bich, the third event didn't count
http://www.fskate.ru/info/rusnat/2016/sel_pairs/
In fact, if you look at previous years, it is only exception when someone does three events. Everyone does only two, so I think three events are not allowed unless in some exceptional circumstances, orherwise everyone would be doing three.
In juniors some pairs last year did three, but they qualified already, so it was just for getting competitive experience rather than for qualifying. I think in pairs the rules are more lax because threre was not so many pairs, especially senior pairs. Pairs is the only discipline where the skaters are allowed to do both junior Russian cup events and senior Russian cups within one season. In ladies, for example, they have to choose if they want to do Junior or senior Russian cup events. In pairs, you can do both.
Zhuk/Britkov did only two events. Two junior and two senior. There were three junior pairs that did three events, but two of those were already qualified by having JGP event, so they definitely didn't do it for qualification, and the third one is somewhere near the bottom of the qualification table, so I think it was more abour practising competing rather than hoping that they may get to the nationals (with seventh and seventh place, they didn't have a chance of getting to the nationals anyway).
No lady or man (junior or senior) did three events, no senior pairs this year... I think it is safe to say that they are allowed only two events.