1. Simbot issue: No that is not normal. Do you have any 3rd party mods in your game ?
2. Ghost: The item has two purposes. See this for more details: http://www.carls-sims-3-guide.com/lifetimerewards/philosophersstone.php
I can't tell you how to get rid of the ghost though and he should be a regular new member and not take over your Sim. Do you have just one icon ?
3. IF: is the science rabbithole a multi-rabbithole (does it have another purpose then only the science center) ? There a bug with those. It helps to replace the rabbithole with one of the single ones. You will need to get the opportunity again though.
