Board milling is one of the most widespread methods for manufacturing printed circuit boards from low frequencies to the microwave and millimeter wave range. In this contribution, the detrimental effect of defects typical of printed circuit board plotters has been investigated. In detail, a systematic frequency shift in the circuit performance has been observed both in terms of S21 and S11 parameters. The performance degradation has been analyzed and attributed to the inaccurate milling depth, which is typical of many plotters, particularly for less recent models. After the conductor removal step, the unwanted milling of dielectric material changes the electrical properties of the microstrip structure, in turn affecting the circuit performance. This circumstance has been investigated by means of electromagnetic simulations performed on the real case study of a parallel coupled lines filter. Therefore, a filter prototype has been realized and measured to confirm the simulated results. This study can be beneficial to those professionals involved in the design and realization of microwave and millimeter waves circuits with board milling machines.