Can of worms, over here please!
First, there is no such thing as perfect intonation. There is Just Intonation (based on overtones), Equal Temperament (based on calculation), Pythagorean Tuning (based on fourths), Meantone Temperament. If you want to sound multiple notes at the same time (as in chords) and change keys pretty often, Equal Temperament was and is the way to go: each note slightly off, so that chords work. Bach's well-tempered clavier was a bunch of tunes that demonstrated how such a tuning allowed to play tunes in vastly different keys on the same keyboard. In short: perfect pitch notes don't always give the best result, and our electronic tuners therefor usually choose one of the above methods in our place.
Second, frets are always parallel. You can calculate the perfect placement for a fourth fret on the third string, but that isn't necessarily the same location for a perfect note on the first string. Compensating the saddle (making them slightly oblique) helps a little bit. Some guitarist use zigzag-like or fanned frets, but I've never seen them on ukuleles.
Third, strings are almost as important for intonation as frets. Fatter gauges or higher tension influence how far off the notes seem.
Fourth, there is the amount of stretching of the string by the player. On a high action ukulele, or with a player with a strong grip, the tuning on the higher frets easily goes way too high. In the last issue of the Fretboard Journal there are very nice stories about how Rev. Gary Davis, the master of ragtime guitar, devised his own tuning - he did stick to what we call standard tuning, but 'sweetened' it to his style.
Back to your question. It could be wrong, but I doubt it. Use a very light touch to check, see what kind of tuner you use and read the manual to understand which standards it uses to give you the green light, check if all four strings are off at the fourth but not at the fifth fret, and sometimes up to 5% off can sound better than perfect. Only then would I say it's a faulty construction.