The usual culprit is that your printer is not running at the speed you told it to.
A profile asking for 300 mm/s at 0.2 mm layers and 0.45 mm lines demands 27 mm³/s of flow. Put that through a hotend that can melt 12, and the machine runs at 133 mm/s instead. The part takes 3.09 hours rather than the 2.76 the flow would have given.
The slicer's estimate assumed the commanded speed. The machine could not deliver it.
The five things that eat the difference
- The flow ceiling, as above. This is the big one and it grows with layer height and line width.
- Acceleration. A short segment never reaches its commanded speed. On a part full of small features, the average speed can be a fraction of the setting, and firmware limits on acceleration and jerk decide it rather than the slicer.
- Outer-wall speed overrides. Most profiles slow perimeters deliberately for surface quality. That is usually the slowest feature on the part and often a large share of the toolpath.
- Cooling holds. Minimum layer time forces the head to wait or slow down on small layers. A tall thin part can spend most of its print waiting rather than moving.
- Travel. Non-printing moves across a full plate, and every retraction and prime around them.
Why the estimate is a planning number
The estimator on this site states an error band of ±30% against a real slicer, and a real slicer has a similar honest band against a real machine. Both are modelling something that firmware ultimately decides in real time.
That is not a defect. "Is this a two-hour or a twenty-hour job" is the question worth answering, and both models answer it well. "Will this be ready at four o'clock" is a question neither can answer.
Getting a figure you can trust
Time one real print and divide by the estimate. That ratio is your machine's correction factor, and applying it to future estimates beats any model, because it silently includes your acceleration limits, your outer-wall settings and your hotend's real capability.
Recompute it after a nozzle change, a firmware update or a profile overhaul — those are the three things that move it.
Check whether your own settings are flow-limited in the print time estimator, and see the speed trade in the print speed guide.