The front office had neither the intention nor the desire to fill every possible hole in the team. They spent their time and effort trying to build a fundamental structure for the team, especially the starting and and relief pitching staff. There was no one out there for a reasonable price that could be expected to make much difference in the short run, and no one that would make difference in the long run, either at third base or in center field.
If they had gotten fortunate (which they still might) and Stewart had been healthy, he would have been much better at third base than those available on the market, and it is still possible that either Valbuena or Stewart could yet do so.
With Baez on the horizen, third base is hardly the place to put your money right now. The same applies to center and left field. If a couple of players have career years, and the Cubs perform well enough that they seem to have a reasonable chance to go to the playoffs, they might look to improve at a position or two. If not, they are still poised to field a much better team next season.