2 needle Pine nearby.

The tree in question sits between this 5 needle Pine and the 2 needle pine in the previous picture.

P. strobus and P. virginiana are not genetically compatible.

The species is in the same section as many of the SE yellow pines. It is quite possible that the bundles of three originated from a natural cross at some point in the past (this tree or in previous generations)? That said, only Sand Pine is known to hybridize with Virginia Pine and it is also a 2 needle pine. ...still a mystery

I was thinking Pinus echinata what we call short leaf pine, also referred to as a form of SE Yellow pine. These are found in our pitch pine (P. Rigida)forests.

The P. echinata does have 2 or 3 needles bundles. The needles are straighter than the tree in question. These had the classic P. Virginiana twist. The larger 2 needle pine nearby had the same type needle but I could find no 3 needle bundles.
Next time I walk there I will look for a short needle pine. The tree in question is only about 5-6 years old so its parents must be nearby.

A hybrid of P. Echinata makes sense. I believe this crosses with P. Rigida. Maybe this is a Rigida x Echinata cross with no Virginiana involved.Yes still a mystery to me.

I recall several P Virginiana having a few 3 needle bundles along w/the usual 2. So it might be normal. From the Silvics manual:

Hybrids of Virginia pine and Ocala sand pine (Pinus clausa var. clausa) can be made under controlled conditions with either species as the seed parent. Controlled crosses of P. virginiana with jack pine (P. banksiana) and lodgepole pine (P. contorta) have not been successful (25).

All 2-needle pines have odd fascicles of 3, typically near the tip of the lead shoot or other vigorous shoots, that's perfectly normal.

Occasional individuals can have a much higher % in 3s, I remember finding a single Pinus brutia in Turkey with about 60% in 3s, among lots of normal 2-needle trees.

On very vigorous specimens you can get fascicles with more than 3 needles around the lead bud, I've found freak fascicles of 4, 5 and even 6 on strong-growing Scots Pine saplings.

Resin

Okay thanks beng and resin. Seems like this could be normal. This was my question. Since beng' had observed them on P. virginiana I was more assured this was what I also was seeing. Now with resins' confirmation I an sure this is what was. Most of the 3 needle bundles where on the new vigorous growth near the apex of the young tree.

Thanks guys you all are a conglomeration of conifer information.