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.
Articuno are about 5'07" (1m70), although in The Symbol Life it is looking to be more like 6'07" (2m).
Bulbasaur are about 2'04" (70cm), in a height like Buizel for example. But during the anime episodes it is definitely not this high. it is shown to be about 1'04 (40cm).
Charizard and Blastoise
Charizard are usually 5'7" (1m75) tall, but Ash's Charizard is slightly taller than that, at about 7'00 (2m10) tall. Ironically enough, it is shown in Charizard's Burning Ambition that Ash's Charizard is rather small when compared with other Charizard. Blastoise are also taller than what they should be. They are normally 5'03" (1m60) tall, but in all of their appearances in the anime - they appear closer to 6'03" (1m90).
Croagunk are generally 2'04" (70cm) in height, but in the anime it is looking to be more like 1'04" (40cm).
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.
Electrode are normally 3'11" (1m20), but in What You Seed is What You Get! it is seen in the same height like Slugma, in 2'04" (70cm).
Floatzel are generally 3'07" (1m10) in height, but in A Crasher Course in Power! , when it was standing in front of Buizel in was shown to be about 4'03" (1m30).
Forretress are about 3'11" (1m20), but in all of its appearances in the anime, it is shown to be 1'08" (50cm).
Gabite are normally 4'07" (1m40) 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.
Gengar are shown to be 4'11" (1m50), but in all of its appearances in the anime, it is shown to be 3'07" (1m10).
Golduck are about 5'07" (1m70), although in Like It or Lup It! when it was standing near Ludicolo, it was shown to be about 3'03" (1m).
Glalie are shown to be 4'11" (1m50). Ash's Glalie is extremely small for compared to others of its species. Its size appears to be closer to 2'00" (60cm).
Grovyle and Combusken
While normally Grovyle and Combusken are about 2'11" (90cm), Ash's Grovyle and May's Combusken appears to be much larger, being almost as tall as Ash and May. Assuming that Ash is about 5' (1m50), that estimates Grovyle and Combusken to be around 4'0" (1m20). The other Grovyle that have appeared were around this size as well.
Hariyama are shown to be 7'07" (2m30). However, Brawly's Hariyama is extremely small for its species. In Brave The Wave!, it appears to be around 4'11" (1m50).
Lombre are shown to be 3'11" (1m20). Brock's Lombre appears to be shorter than that height, and looking to be more around 2'07 (80cm).
Metagross are normally 5'03" (1m60), but Tyson's seems shorter than this in Choose It or Lose It!. It's shown more likely 2'11" (90cm). Another Metagross appeared in Noodles Roaming Off! and shown to be higher even than James, about 6'03" (1m90).
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 2'00 (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.
Pidgeotto are normally 3'07" (1m10), although during the series it appears to be only 2'04" (70cm).
Rapidash are normally 5'07". However, in Ash's flashback in Strategy Begins at Home!, 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 Adventures both featured the Pokémon at its actual smaller 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.
Smeargle are about 3'11" (1m20), although in Art of Pokémon it is shown to be 2'04" (70cm).
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 1'00" (30cm), 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.