When I go to the “Advancement” pane in the Character Builder, it shows a table indicating that Tier 1 characters (levels 1-5) have a max skill rank of 2. However, the character builder doesn’t enforce this; it happily lets me add additional ranks in skills.
I can imagine cases where a GM might want to allow an exception to the rules, so perhaps the tool should still allow it, but it seems like there should be some indication that you’re going beyond the limit. Otherwise, it’s very easy for players to unintentionally break the skill ranks limit.