Some possibilities: this is the last slide of your file? Have a look at the Preferences, Project, Start and End. You'll see that the default setting is to fade out at the end of the project. Try to turn that off.
There is also a transition possibility for the slides themselves (Properties, General accordion) but normally that is set to No Transition.
A last possibility: some of the objects on the slide have a fade out transition, you'll have to look in the Transition accordion in the Properties panel for the objects. Mostly I turn all those object transitions off in the Object Style Manager before opening a project, so that they will be gone forever. I prefer to turn a possible transition on myself, but default here is again a lot of objects with Fade in and Fade out transition.
In addition to what Lilybiri offered I'll also add this.
Look at the slides where this is happening. Odds are you will find a Button or Click Box object that is pausing the slide while objects are fading in or out of view.
Sure, you can do as Lilybiri is suggesting and disable the transition. But you may also work another way. My own preferred way of dealing with this situation is to ignore changing the transitions and simply more precisely control exactly when the slide pauses by adjusting the pause point of a Button or the end point of a Click Box so they don't pause during a fade.
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I had a similar issue... it turned out that the pauses for my continue buttons were stopping in the middle of the transition. Starting the pause earlier fixed the issue.