oh no, we’re being attacked by terrible monsters made out of fluffy clouds! how can we possibly overcome them?

@Background Pony #5C12
 
The show writers do not actively take the events of the comics into account when writing episodes, so occasionally a contradiction will occur. The stories of the comics are vetted by Hasbro, however, so occasionally events of the comics will be influenced by Hasbro’s wishes. One of the main things they do is make sure that the stories the show and comics are doing aren’t too similar. Inconsistencies like the one you mentioned are easily ignored.
 
M.A. Larson stated in an interview recently that Hasbro is taking a more hands-off approach to the writing of the show, however, so it remains to be seen if the same is or will be true with the comics. This is interesting given Hasbro’s goal of the last few years of bringing the various licenses (toys, shows, comics, movies, video games, etc) closer together within each property (Transformers, D&D, GI Joe, etc). This is also likely a part of Meghan McCarthy’s new position as Director for Girls’ Stories (or whatever the exact title was). She may now be the person at Hasbro who gives the comic storylines the thumbs-up or down.
 
Andy Price and Katie Cook’s OCs appeared in Princess Spike as background ponies (though that is more of an artist-to-artist favor). G.M. Berrow writes for the show as well as writing numerous childrens’ books about the series. In one of her books, she referenced Tiberius, Luna’s pet opossum, who up until then had only appeared in the comics.
 
Given all that, it’s theoretically possible that comic events may someday tie in more with the show, or it may become more of a two-way street. The main problem is if something from the comics is to be introduced to the show, it will need to be explained again for the show viewers who may not be familiar with it from the comics, or it will lead to a lot of confusion.

@Masem  
Yes but in Cutie Re-Mark, Twilight makes sure to make it sound like she hasn’t seen Sombra after the Crystal Empire episode. That’s not possible if the comics were canon as this shows quite clearly that it is pre-cutie mark.

@Background Pony #5C12  
If you are talking the lack of cutie marks, the comics do tend to run behind the show, and they’ve said the cutie mark change won’t come in until issue 41.

…Did this page just make the comics noncanon? Or at least this addition.

@PonyPon  
yeah this was awesome

Er. Why is Sweetie pulling? Shouldn’t Scootaloo do that?
 
Or is the comic hinting that even Sweetie Belle has a higher chance to get off the ground?

This comic is getting good now well it’s about time.

Rarity and Applejack are proud.

Okay, that pretty cool.