Total electron content (TEC) and L‐band scintillations measured by several networks of GPS and GNSS receivers that operate in South and Central America and the Caribbean region are used to observe the morphology of the equatorial ionization anomaly (EIA), examine the evolution of plasma bubbles, and investigate the enhancement of L‐band scintillations that occurred on February 12 and 13, 2016. A few weak and short magnetic storms developed these days, and a minor sudden stratospheric warming (SSW) event was initiated a few days before. During these unusual conditions, TEC maps reported a split of the otherwise continuous crests of the EIA and the formation of a large‐scale (thousands of kilometers) almost‐circular structure. The western part of the southern crest faded, and a north‐south aligned segment developed near the center of the South American continent, joining the north and south crests of the EIA, forming an anomaly that resembled a closed loop on the eastern side of the continent. Concurrently with the anomaly events, several GPS stations reported increases in the L‐band scintillation index from 0.4 to values greater than 1. We analyzed TEC values from receivers between ±6° from the magnetic equator to identify and follow TEC depletions associated with plasma bubbles when they reach different stations. Although the magnetic activity was moderate (Kp = 3°), we believe that the anomaly redistribution and the scintillation enhancements are not related to a prompt penetration electric field but to enhancing the semidiurnal lunar tide propitiated by the onset of the minor SSW event. We found that depending on the lunar tide phase cycle, the neutral wind's meridional component can augment sub‐km scale irregularities and enhance L‐band scintillations through the wind gradient instability when U·∇ $\nabla $n < 0 or the action of wind gradients (∇ $\nabla $U) within the bubbles. Our observations imply that the SSW event enables prominent changes in the thermosphere wind system at F‐region altitudes.