If you visit forums for other editors you will see that issues are not exclusive to Videopad. In this case it's tough to single out a specific cause, except those mentioned above.
In general, keep things as simple as possible. It's a learning curve.😉
In most cases there's no need for multiple sequences. Load only the files that will be used - saves time.
To add a clip, import it into the bin, click on it to preview, drag the cursor to the IN point and press the SET IN button. Drag to the OUT point and press the SET OUT button. Then either drag the clip to the timeline or click the caret in the ADD button (under the preview window) to place it where desired.
Or drag the untrimmed clip to the timeline, then trim it there.
As you build a project, check it for errors from time to time by exporting the existing portion. Then you can spot and fix problems before they become a crisis.
And of course, Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite. From the HOME tab, that choice is available by clicking the caret to the right of the Save Project button on the toolbar.
A segment can be exported by dragging the middle of the cursor right or left, to create a blue selection area. Right-click that area and Export Selected Region. 
For complex projects, use the 64-bit version of VP.
For licensed users upgrades are free for up to six months from purchase date. After that, VP will continue to fully function but a fee will be required in order to register the newest. Retain your old install file and registration info.
For tutorials, there's a Tutorials link at the top of this forum. Good luck!