Chemotaxis, the movement of an organism in response to a chemical stimulus, is a typical feature of many microbiological systems. In particular, the social amoeba Disctyostelium discoideum is widely used as a model organism, but it is not still clear how it behaves in heterogeneous environments. A few models focused on mechanical features have already addressed the question; however, we propose that phenomenological models focusing on the dynamics may provide new meaningful data. Consequently, by means of a specific Multi-agent system model, we studied the dynamical features emerging from complex social interactions among individuals belonging to amoeboids colonies. After defining an appropriate metric to perform meaningful measurements, we found that: a) obstacles play the role of local topological perturbation, as they alter the flux of chemical signals; b) that obstacle that physically block the cellular motion as well as the chemicals elicit dynamical evolutions that are not statistically distinguishable from the case where obstacles that do not interfere physically with said motion; c) that fluctuations of the dynamics can lead to better exploration of the physical space, thus preventing multiple stable aggregates. From previous results, we may speculate about the fact that chemotactic cells, in many cases, can avoid obstacles by simply following the altered chemical gradient: social interactions seem to be sufficient to guarantee the aggregation of the whole colony past numerous obstacles. It is then unlikely that cells have developed special mechanisms to cope with the presence of topological perturbation sources. Nevertheless, we suggest that further studies can provide better understanding and that, in order to gain deeper knowledge, mechanical models should be coupled with phenomenological, system-oriented ones.