Even though we didn't rip any continents apart this time, we did change the environment in some areas. Ocean life that needs the depths will vacate areas where mountains are building. Creatures that need non-salt water will survive better closer to drinkable water sources such as rivers and lakes. Bug life thrives in marshy areas, so any land that raises into mountains becomes less buzzing and stinging, not to mention that creatures that need marshes will migrate to areas that aren't rising out of the waters. All of this creature migration creates a number of issues.
Many animals try to maintain a certain amount of territory.
There is also the issue of food. If many marsh plant eaters suddenly pack into a shrinking marsh area because the higher ground is not suitable for them, then some species may die out or at the very least there will be a change in overall population. Get too many predators packed together and you may end up with a food shortage, or fights between the creatures as they press for territory or have other interspecies conflicts. More mountains mean more room though for creatures that don't thrive in the marshes. The higher a species thrives, the more exclusive a territory it gets.