Of course, we cannot know this for sure since the Marshall Court did not write decisions saying "we will not invalidate anymore laws because..." However, political scientists would argue that the Marshall Court declined to act because it did not want to lose its legitimacy.
The power of judicial review was, of course, not set out in the Constitution. The Marshall Court took the power for itself in Marbury v. Madison. This was truly a bold move and further invalidations could have provoked a great deal of opposition in Congress. This would particularly have been true in later years as the Congress was dominated by Democrats while Marshall and his court were still heavily influenced by old Federalist ideas.
If the Court had continued to invalidate laws, they could have undermined their power. They could have made Congress very angry and provoked a showdown between the branches. Since the idea of judicial review was still very new, it would not have been clear that the Court would have won this battle.
To political scientists, the Court needed to be somewhat reticent so that it would not overreach its power and, by doing so, lose it. The Court would have worried that using its power would bring it into conflict with Congress and the Court might lose its power in that struggle.