From Bulbapedia, the community-driven Pokémon encyclopedia.
Aside from giant Pokémon, many Pokémon in the Pokémon anime suffer from large size discrepancies between the information given in the Pokémon games' Pokédex and their actual animated presentation. These Pokémon are apparently "normal sized" as far as the anime's universe is concerned.
This may be a style or aesthetic decision, a case of the writers not checking the information in detail, or for story purposes.
Some of the most notable size discrepancies will be noted below.
Charizard are usually 5'7" (1m75) tall, but Ash's Charizard is slightly taller than that, at about 7' (2m10) tall. Ironically enough, it is shown in Charizard's Burning Ambition that Ash's Charizard is rather small when compared with other Charizard.
Dunsparce are normally 4'11" (1m30) in height, approximately the height of Ash. In Following a Maiden's Voyage!, they appear to be shorter than a Pidgey. However, like with Ekans, the height may refer to length.
Ekans are shown to be 6'7" (2m), exactly the same height as Mewtwo; however, when Jessie's Arbok was an Ekans, it stood no higher than her waist. However, its height may actually refer to its body length instead.
Gabite are normally 4'07" (1m25) in height, but Ursula's Gabite from Another One Gabites the Dust! was at least a couple inches taller than Ash, Dawn, and Ursula, who are about 5'0" (1m50) tall.
While normally Grovyle are about 2'11" (89cm), Ash's Grovyle appears to be much larger, being almost as tall as Ash. Assuming that Ash is about 5' (1m50), that estimates Grovyle to be around 4'0" (1m20). The other Grovyle that have appeared were around this size as well.
Noctowl are about 5'3" (1m60), approaching average human height. Ash's Noctowl, however, is extremely small for that size, looking to be more around 2' (60cm). Although it's been mentioned that Ash's Noctowl is unusually small, the other two Noctowl that have appeared in the anime don't seem to be more than 4' tall.
Nosepass are normally 3'3" (1m) in height. However, in the episode Nosepass debuted in, Nosepass is far bigger than it is supposed to be, at about 5'6" (1m70) compared to the normal Nosepass.
Rapidash are normally 5'07". However, in Ash's flashback in DP138, it was shown to be about 3'03" tall, about the size of a Ponyta.
One of the more renowned changes in size is in Roselia, which are extremely small - only about a foot (30cm) tall. However, the Roselia in the anime come up to a 10-year old's waist. An estimate would put the anime incarnation of them at about 3' (90cm) tall. This caused much confusion when Pokémon Colosseum and Pokémon Special both featured the Pokémon at its actual "midget" (to fans of the anime) size.
Jessie's Seviper appears to change sizes during the series, sometimes even in the same episode. For example, when it made its debut, it was shorter than Jessie. However, it has also been shown as being taller than her, which according to the Pokédex it should be. However, its height may actually refer to its body length instead.
Wailmer are generally 6'07" (1m85) in height, although the one in Leading a Stray! was shown to be more than twice the size of Ash, who is approximately 5'0" (1m50) tall.
Whismur are very small Pokémon at around 2'00" (60cm). In A Pokéblock Party!, a Whismur was around the size of 2'00", and was noticeably not much larger than Max's head. A second Whismur appeared in Pinch Healing! and, while standing, came up to Max's neck.
Sudowoodo are normally 3'11" (1m20), but Brock's Sudowoodo seems higher than Dawn's Ambipom (That also is 3'11") in Hungry for the Good Life!. It approximately seems 4'03 (1m30) tall.