There are many challenges in maintaining the sustainability of microgrids in remote areas, one of them being early failures of the components. Due to limited access and resources, solutions that are quick, cheap, and easily obtainable are used to fix the failed components. Therefore, systems with ad-hoc modifications are typically found, which are deemed necessary for the system operation. Through on-site voltage and current measurements, this paper investigates the additional risk of failure due to electromagnetic interference (EMI) that is introduced by necessary ad-hoc modifications in a remote microgrid in Indonesia. There are two separate microgrids (microgrid 1 and 2) with a desalination system connected to microgrid 1. Failures were found, which required the desalination system to be connected to microgrid 2. The results show that the modification in microgrid 2 reduced the efficiency of the battery inverter, increased voltage harmonics, and made the microgrid more susceptible to an inrush current. The findings corroborate the importance of remote EMI measurements and monitoring to get insight into potential risks and undertake timely measures. This is crucial, especially in remote areas where repair and replacement could be costly.