The confusion appears to have been accidental, but as soon as it was noticed 'ali' was introduced as an alternative to 'ale'. It is not used consistently; Sonja still uses 'ale', other 'ali' and many flip back and forth. The mistaken use of one of the al's for the other is probably the most common straightforward word replacement error (the second seems to be confusion of 'loje' and 'laso'). (One virtue of one big number solution was that it gave a totally new word for zero.)
'Ali' and 'ala' are about as distinct as you can get in that position in tp ('alu' might be better) and different dialects, brought over from native languages, affect the whole considerably (my English tends to reduce all unstressed vowels toward the /a/ In "sofa", for example). Since I ( and most tapers) have little experience with spoken tp, it is hard to say how awful the problem is/would be. But just one flub would be quite significant (as someone remarked "the worst minimal pair ever").
There are a number of other word pairs that present potential problems as more actual spoken example become available. For example, u and w seem to draw neighboring sounds on so that 'suwl', 'suli' and 'sewi' sound a lot alike and meeting it and native languages produce indecipherable results ("shoe en" for 'kiwen' being my favorite so far). Hopefully as there is more spoken tp around, some adjustments in word form will take place (though I wonder why no thought was given to that -- a well- known problem in constructed languages -- at the beginning).