When you draw a line with the pencil tool, and let go of the mouse, the line completes. If you proceed to try to continue the line by clicking on the end node and continuing to draw, each line will be a separate object.
It would be best, if after drawing a complete line, clicking on the end node of either side would allow you to continue drawing on the same object.
Also, when you draw a complete shape, it should automatically close when the two ends touch. Currently they are disjoined and will snap together when the last node is hovered over the first, but to save time, this should just happen while drawing the original line.