This has nothing to do with independent increments. The Markov property works when we have an equality assumption for the "present", e.g. $$P(X_3\in A\mid X_2 = x, X_1\in B) = P(X_3\in A\mid X_2 = x). $$ However, when there is a range of values, as in your question, it is possible that the condition on the "past" value $X_1$ makes some particular values of the "present" $X_2$ more probable.
For example, let $X$ be a Poisson process. Consider e.g. the probability $$ P(X_3 \in\\{100,50\\}\mid X_2\in\\{100,1\\}, X_1>50). $$ Clearly, it is equal to $$ P(X_3 \in\\{100,50\\}\mid X_2=100, X_1>50) = P(X_3 =100\mid X_2=100) = e^{-1}. $$ On the other hand, the conditional probability $$ P(X_3 \in\\{100,50\\}\mid X_2\in\\{100,1\\}) $$ is close to $P(X_3 \in\\{100,50\\}\mid X_2=1)$ (since $X_2=100$ is highly unlikely) and is extremely small. Consequently, $$ P(X_3 \in\\{100,50\\}\mid X_2\in\\{100,1\\}) \
eq P(X_3 \in\\{100,50\\}\mid X_2\in\\{100,1\\}, X_1>50). $$