In the Dalek Invasion of Earth, why would the Doctor suggest that his first adventure with them may have been "millions of years in the future"? When he first met the Daleks on Skaro they were limited to movement within the city, while on Earth they could move freely.
The first Dalek story showed them being destroyed, so it was necessary to explain why they were still around in "The Dalek Invasion of Earth." That's really all it is.
The explanation that the Daleks had previously been spacefaring conquerors before being confined to their city is weak, but there are no outright contradictions or timey-wimey ball involved.
Out of universe: The Daleks proved much more popular that expected in their first appearance, and a way had to be found to keep them going for future stories.
In universe: The actual timeline of the Daleks is debated and confused, unsurprisingly. One simple explanation is that the Doctor was right, and the invasion happened whilst the Dalek Empire was at a peak, and that a gradual decline happened until they retreat back to Skaro and are eventually destroyed (in this timeline).
It's also worth noting that, with both Time Lords and Daleks capable of time travel and interfering later on, unclear inconsistencies to the timeline could have been ripple effects from attempts to start, win or prevent the Time War by future generations.