When do the Kodomo no Jikan OVA side stories take place?
Wikipedia lists the 3 OVA episodes in question as follows:


Yasumi Jikan '~Anata ga Watashi ni Kureta Mono~' is between the 4th and 5th episodes of the 1st season.
Kuro-chan to Shiro-chan occurs between the 1st and 2nd episodes of the 2nd season (which is a 3-episode OVA season)
Kodomo no Natsu Jikan takes place after the end of the second season.