I experienced something similar. On the 3rd playthrough of the potioncraft the entire board froze. The timer kept going but I couldn't click on or move any of the potion items.
Did you manage to fix it ? have same issue in the first potioncraft lessen timer stops but you can keep playing and some orb are lagging
I haven't really played since then. My presumption is that given there haven't been updates, it probably is not resolved.