I have temp in my house set for 72 degrees (small baby). Sometimes I wake up in the middle of the night or just in the morning and the temp in the house is 69 degrees! Why hasn't the furnace kicked on? Bad thermastat or is it something with my furnace?

First of all, 69* isn't going to hurt the baby. Some thermostats are not that accurate. I have seen them off by as much as 5 or 6 degrees. This is especially true for non digital stats.