The yellow color is due to very small amounts of harmaline still remaining dissolved at pH 10.5.  If filtered and then based with copious NaOH, the solution will turn clear and a tiny fluffy layer of harmaline precipitate will form.

The pH of your tap water means that you have "hard" water.  Small amounts of calcium carbonate could get trapped in the freebase while washing.  These are harmless and there would only be minute quantities present.  You can wash with store bought demineralized water instead if you want to prevent this.