は and す pronunciation
In the courses (mainly Hiragana 1 when you're first learning the kana), は is pronounced "wa", even though it is supposed to be "ha". Of course, は's use as a topic marker would warrant pronouncing it "wa", but all the same, when it's a part of an actual word it's pronounced "ha". This can throw those who don't know the difference off; for example, should おはよう be pronounced "ohayou" or "owayou"?
す has an issue along the same lines as well. Its Romaji counterpart is "su", yet it is pronounced "s"; the "u" is silent. The problem with this is that omitting the vowel in this case (and in a few other kana) I believe is purely stylistic; some would pronounce it "arigatogozaimas", and others would pronounce it "arigatogozaimasu". Some would say "itadakimas", some would say "itadakimasu", and so on and so forth.Forcing the learner to take a specific branch in this stylistic pattern—the branch which, might I add, differs from す's actual pronounciation—seems silly.
In my mind, は should be pronounced "ha" when alone (and there should then be a note either below the lesson info or upon mousing over it saying that it is pronounced "wa" when used as a topic marker), and す should always be pronounced "su" (and with a note explaining the stylistic difference), but that's just my opinion. What are your thoughts?
The "u" in す is not silent, but rather tends to be devoiced in certain positions. This can actually occur with other vowels too. This devoicing of vowels isn't phonetically required, though, and from what I know, completely pronouncing all of the syllables results in the speaker sounding more clear and eloquent.
I'm sure they realize the problem with は, though and intend to fix it before the end of beta testing.
As @No--One has mentioned, the the "u" in す is not silent, but merely voiceless when it appears at the end of words. That being said, the "u" is pronounced when trying to be emphatic or very polite.
However, the "u" in す is generally pronounced when the phoneme appears at the beginning of a word (there are exceptions). Thus the "u" is voiced in すいようび (水曜日、"Wednesday") , すごく（凄く, "very") or すばらしい (素晴らしい, "amazing"), but not, for example, in the adjective すてきな (素敵な, lovely).