As a new GM, I find the problem isn't so much with inconsistency in the rules, but with difficulty clarifying a rule in a short time frame. The index is amazing, but the full answer isn't always in one place, so the clarification often ends up being only half of the story. That does lead to some inconsistency, but my players don't seem to care. So for us it hasn't been an issue.
As others have pointed out, the inconsistencies occur more when you include the supplements. I'm playing mainly from the CRB and Rigger 5, with a little Data Trails mixed in. Generally I don't any find inconsistencies in the rules, though sometimes I find holes with no answer. I'd imagine somewhere there is a supplement that addresses those holes. As the GM, those holes tend to get ruled in a consistent manner, because my guess at the RAI tends to be the same each time.
Overall though, at my table, with my group, inconsistencies aren't a big deal. My players aren't min/maxing, they are only familiar with the rules on a basic level. They want to accomplish their goals using things from their character sheet that were interesting to them at creation. As long as they get to do that, they don't worry too much about what worked this time versus last time. To be fair, I don't have any magic users in the group, but I do have a Technomancer. Finding consistency for a TM who is using his ideas creatively can be a challenge.
Generally though, if people are having fun, they won't get caught up in minutia and rules-lawyering. With the caveat that for some people, the only way for them to have fun is by rules-laywering. If they care about their character being perfectly capable of everything they envision, more so than they care about playing through a fun story, then there's not much you can do about that. I remember some arguments on the D&D forums years ago, during 3.5e, that would make SR5's inconsistencies look like minor stumbles. In the end it came down to massive over-complexity. Shadowrun is complex, so it will always have more susceptibility to inconsistencies. Some will be bothered by that, some will not.