Study of the causes of disrupted ionospheric E layers at middle latitudes. The irregularities described here are organized accordingly to the Richardson (Ri) number, starting from negative, to less than one quarter, to larger than one. Since Ri is a function of the neutral winds, a methodology to estimate the mesosphere and lower thermosphere (MLT) neutral winds between 95 - 130 km altitude is applied for data collected during the incoherent scatter radar (ISR) coordinated ``World Day''' campaigns at Arecibo. The methodology reflects the physical coupling between the neutral atmosphere and the ionosphere at E-layer heights. The method is compared with previous attempts to calculate the neutral winds at the Arecibo Observatory. The methodology is validated using error analysis and considering possible data contamination due to gravity waves. Temperature profiles, electric fields, and ion composition are also estimated. Using those parameters, the subsequent sections of the dissertation study irregularities observed in the neutral atmosphere in the MLT region during the day. Analysis of temperature variations following convective instability events shows that most of the days have broad unstable regions, where the condition needed to develop this kind of instability is present (buoyancy frequency N^2<0). During these days, disturbed temperature profiles are observed. Dynamic instability studies show zones with 01), where Ro is the Rossby number. Finally, studies of nocturnal quasi-periodic (QP) echoes are presented to investigate their dynamic instability origin. The irregularities produced different disruptions in the E layer. Convective instability events can create broken layers. Dynamic instabilities generate billow behavior and bifurcation that can also lead to broken layers. Planetary-wave effects can explain the rotational neutral winds and changes in their rotational direction.