In regards to what Markus and McFeely said regarding AOS and Civil War, I'm going to put what I posted on IMDb (yes, IMDb) regarding their quotes...
Given what was said (and reading Collider's transcript of the set visit), I think this simply highlights the main problem when it comes to the films referencing the tv shows and why they haven't been able to have it happen yet: the differential in production time between the two mediums (film vs tv).
The scripts for the films can start getting worked on years in advance before the film is slated to be released (I believe Markus and McFeely started working on the Civil War script in late 2013? - so season 1 of Agents of SHIELD was only just starting while they were working on a film that wasn't going to come out until near the end of Season 3).
Conversely, the turnaround time on a standard 22 episode tv show is much smaller. Episodes and scripts for later in season "x" are still being written and filmed even after the season has already started airing (a large reason tv shows will often take breaks during the course of the season is so they can 'catch up' on production/give themselves a buffer zone to work with).
So it's much more difficult for the film side to incorporate content into their script(s) when - as they get closer to filming the movie and have to start locking stuff down - that content from the tv show may not have even been written yet (or may not even be a solidified idea yet in the minds of the tv shows showrunners).
When Civil War started filming (and so the script was probably pretty finalized aside from a few tweaks here or there), Agents of SHIELD hadn't even been renewed for Season 3 yet.
Finally, remember that the set visits happened last year (I believe in July), so they still had a month of filming to do, not to mention the reshoots that happened in January-February. There's always the *possibility* that something could have been added in after they gave those interviews (but then again, perhaps not). We won't know for sure until the film comes out.
That's my take on it.