Could be a million things.
I've never used a pygmy meter professionally, but something you need to keep in mind is they're not measuring average velocity of the flow. They're measuring a point velocity wherever you take the measurement. Because of the no-slip condition, the velocity they measure is going to be lower nearer the banks and nearer the bottom, and higher towards the middle. If you're trying to approximate the flow rate of a creek, you need to do one of two things:
a) Estimate the average velocity across the creek, and multiply that by the cross sectional area of the creek. Estimating that average really comes down to engineer's best judgment, which will end up with some wiggle room.
b) You could get a point velocity at many different spots in the cross section, and integrate over the cross sectional area to get a true flow rate. That's spreadsheet calculus, might be beyond your scope, but it's the most accurate way of doing it conceptually.
If you opt for a) then there's going to be some wiggle in your data, and that wiggle could make it look like the flow goes down. Another thing to think of, is how good is your bank survey? If you're determining flow rate by multiplying velocity by area, and the survey isn't exact, then the area isn't exact and it'll introduce an error into your calculations.
The second thing to realize is what SMIAH said - creeks don't necessarily flow in a steady state. Lets say you measure on a Tuesday, and there was rain on a Monday. If the hydrograph is tailing off the day you measure, and you measured an upstream section before a downstream section, then the downstream section might legitimately have less flow.
Third is the idea of diversions or whatnot. If you're in coastal soils, or karst, or out in the Arizona desert or something, then you might actually have less flow, because water is leaking into the soil or evaporating. Are there any industrial or municipal users extracting water from the flow? Etc.
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