This question was brought up several times turning out to be very delicate and confusing subject to talk about.
Especially when 14th movie Pokemon Whize and Black; Victini and Reshiram, Victini and Zekrom for first time in poemon history contained two different reality and versions which differs in several aspects from each other canon wise. Making it all that more confusing if they are meant to be story incorporated in timeline and events Best Wishes series followed.
However one excample doesn't make rule or pattern, its just exception to rule.
In general all pokemon movies can be considered canon 100% with several of them receiving references in main pokemon series through Ash and friends journey over past 16 years.
Here are some of them:
1st movie "Mewtwo Strikes Back": Mewtwo nearly killing Giovanni and battle betzween Giovanni and Gary was showerd. All of this took place in pokemon series during time Ash went to challenge Viridian gym.
2nd movie "Power of One": Ash and friends mention during Silver arc in Whirl Islands side adventure how they already saw Lugia once in Orange Islands which took place around time 2nd movie aired)
3rd movie "Spell of Unown": (dont hold me on words about this but if i recall right Ash mrentioned how they already met Entei once during episode"Entei at your own Risk" from Johto series(only time they met Entei prior to that happened in molvie as manifestation of Unknown illusion).
But much stronger evidence was demonstrated when Liza and Charific valley from anime was showed in movie with Charizard deciding to leave and help Ash out.
4th movie "Celebii: Voice of the Forest": Ash saw Suicune and made reference to prof. Oak how he already met Suicune before(happened at start of Johto)
7th movie "Destiny Deoxys": LaRousse City from movie was mentioned as May rival Drew hometown in anime
8th movie "Lucario and the Mystery of Mew": special guardian aura sir Aaron and Ash showed in movie became continuous thing coming up several times in main series. During episodes "The Keystone pops"(featuring Spirtomb ) and in "Pokemon Ranger and the kidnapped Rolu" two part episodes. Followed with Riley and Lucaropo appearances in Team Galactic episodes.
10th movie "Rise of Darkrai": Lunar wing Dawn bought in movie appeared in episode "Sleepless pre Battle" from Sinnoh series when Darkrai and Cresselia appeared. Minor thing but in episode "Sphere of Influence" in one of show displays space-time towers from that movie.
Those are examples i remember, if there exist more feel free to correct me.
Truth is that writers aren't always consistent and faithful in properly reflecting events and plots which happened before on screen and anime in general has pretty shaky continuity and connection to previous characters and impacts left on story before. As such possibly leading to different impression.
However based on all this references and throwbacks to movies happening in pokemon series its safe to make inference how events and timeline in movies are entangled within story of main anime. By covering aspects of journey which takes place between certain episodes based on items and remarks to scenes and incidents which were brought up at times in regular episodes.
Thus leading to logical and sacrosant deduction how pokemon movies generally speaking in my opinion are indeed meant to be interpretented as canon set in same timeline and universe as main show follows. They could in a way be viewed as some sort of complementation to main series story covering plots and events which otherwise couldn't have been showed in regular episodes, due to time constraints and predefined path through which tale would unfold and be told out to viewers.
