Donald Trump got a significant bump from wrapping up the Republican nomination a couple of weeks ago, while Hillary Clinton—even though she will be the nominee—still has a strong opponent in the race who is making the case against her, as well as against the fairness of the nomination process itself.
Bernie Sanders has won most of the races this past month, and the chaos at the recent Nevada Democratic Convention only increased the bad blood. Negative feelings toward Clinton felt by some Sanders' supporters are, without question, affecting the Clinton v. Trump poll numbers. Some percentage of Sanders voters are currently saying they are undecided, or voting for Trump or even, if there’s such an option in a given poll, "other" (i.e., Sanders).
When the Democratic race is settled and both nominees are in a similar position regarding the supporters of their primary opponents, we'll have a much better sense of where this race stands. It will likely look much more like it did about six weeks ago, before Trump swept the Northeast and pretty much wrapped things up.
For example in 2008, while both nomination races were going on throughout February, the polling averages showed an Obama lead over McCain, but McCain got a bump and went ahead after securing the Republican nomination in early March. Obama began closing in on McCain and went past him a few weeks later in the polling average, after the bump faded and Obama's grasp on the Democratic nomination began to look more secure. When the Democratic race ended and Clinton endorsed him in early June, his lead grew. Other than a few days after the Republican convention in early September, when McCain led by a point or two thanks to his convention bounce, Obama remained ahead from early April right up to the election.