There is conditioning and then there is conditioning.
Those of you playing both football and basketball know you have more muscle mass for football and less for basketball. Weightlifting is different between the two. The muscles required in basketball tend to be longer, smoother, and not as massive.
It affects your play in basketball after having played the football season, and it takes a little time to get the muscles smoothed out. There is more running up and down the court in basketball, and over the season, the muscles adapt to the smoothness of basktetball and lose some of their mass.
If you have observed runners, those that run every day and enter the marathon races, you will note they have little muscle mass. I hate to say it this way, but some marathon runners tend to look a little effeminate due to the excessive running. A lot of running tends to reduce muscle mass.
If a team reduces its weight lifting and increases its running exercises, the players will lose some muscle needed for the rigors of football. Windsprints were always good, because they were short burst of speed increasing quickness. Windsprints did not last that long, and tended not to reduce muscle loss. Steady running will reduce muscle loss.
I don't know the extent of the players running to keep in shape, but too much of it could be detrimental to their strength.
Weight training is good for football players to increase their strength. Being in shape is good, but can be over-rated. The reason for having substitutes and playing a lot of players is to keep the players fresh.
Lifting weights should be adapted to the athlete. A linemen should lift weights differently from a receiver or player requiring quickness. It is well known a muscle bound athlete loses some of his quickness. It is possible our conditioning program is not meeting the needs of the various positions of the athletes on the team.