As a life long comic book fan and collector. I don't think that this will be a major problem with the time line of the MCU for a few reasons. Marvel Movies have already taken some liberties in introducing characters and their back stories how they saw fit (i.e. original members of the Avengers, Ultron, THE MANDARIN, just to name a few).
Taking that into consideration and now looking at Doctor Strange, you cannot have an unlimited awareness of every MCU character whenever a movie is made. We have to give the movie makers some benefit of the doubt to weave a plausible connection between the two or more films and keep it moving. Movies have never and will never be pinpoint accurate compared to their comic book counterparts so I think that a lot of the commentary that we hear should take this into consideration and try to enjoy and critique the film itself that's at hand. Once any adaptation is made then by definition it's not the same as the original.
To date I've enjoyed all of the Marvel movies, some more than others but I can't say that due to the inaccuracies of the timeline or origination of the characters according to the director or producer perspective, that I have not enjoyed the films. I do share in some of the disappointments of these inaccuracies however I try not to let that prevent me from enjoying the movie and seeing if what they did do was good within their own parameters.
I'm very excited to see Doctor Strange. As a kid I thought that he had the most potential of be a realistic character than all of the other favorites of mine. I do have high hopes for this movie and I hope that they get the special effects right!