According to the Schengen rules, the German border guard should have stamped your passport when you arrived, irrespective of you having a long-stay visa. But the consequences for you of not having the stamp are small or nonexistent.
In general the Schengen system depends on entry/exit stamps for documenting how long a traveler has been in the Area, and verifying that he complies with the 90/180 day rule. (There is not currently a common database of entrances and exits that can replace this). However, in your case since you have a long-stay visa, the stamps can't be used for that purpose anyway, since days you spend in Germany under the visa are exempt from the 90-day count. And you never get stamps while traveling between the Schengen countries, so enforcing the 90/180 rule for foreigners with long-stay visas is up to the honor system and extrinsic evidence anyway.
As Aganju says, you might be able to reduce practical troubles by holding on to boarding passes or other documentation for when you traveled. Most likely this documentation will never even be demanded of you, though, since your current status is in effect independently of when you arrived in the Schengen area.