What each source measures
Speed through water normally comes from a log or equivalent sensor. Speed over ground usually comes from GPS and describes movement relative to land.
Current and calibration
The values can differ because of current, direction of movement and instrument errors. A fouled or poorly calibrated log can give unreliable readings.
Use the right input
Identify the source used by each calculation and check units. True wind, performance and track calculations depend on which speed an application uses.
An example with current
The log measures movement through water; GPS estimates movement over ground. Current can make the values differ and direction matters: simply subtracting two numbers without considering vectors is not always sufficient.
When to suspect the sensor
If the log remains fixed or changes unexpectedly, check fouling, connection and calibration according to the manufacturer. Compare trends with GPS while remembering that these are different measurements.