You can have both meth and pseudo in the same batch. Never assume that the reaction proceeds in a formal, precise manner of reducing all the pseudoephedrine to an intermediate before reducing any of the intermediate to meth, then to methamphetamine. A good deal of pseudo will be reduced to an intermediate right at the start of the reaction. Part of that intermediate will be reduced to methamphetamine very early on, as early as fifteen to twenty minutes into the actual reaction. You may encounter the product of reactions that ran for as little as twenty minutes which contain appreciable levels of methamphetamine, and which will keep you awake for a considerable time if you do enough. These will usually include a little bit of pseudo, and a good portion of intermediates. I find these batches, regardless of how clean the pseudo, to be prone to cause jaw clenching.
In my experience the pseudo is most often found in reactions that were insufficient from the start in HI. This usually will be the case where the red phosphorous was inadequate to produce enough HI to reduce all of the pseudo to an intermediate. It also happens with insufficient I2. This is common with lower quality red phosphorous, or "tired" mbrp that is more glass and trash than phosphorous. It can happen with recycled I2 that is not resublimed, or with too-wet I2 from tinc whose weight is not adjusted to compensate for the moisture content. Loss of HI in gas form at the start would have much the same result. These reactions may have some reduction to methamphetamine, but will have a good portion of unreduced pseudoephedrine, and more intermediates. If the shortage of either of Iodine or phosphorous is pronounced, you may have nothing but pseudo and a little intermediate. In reactions which commenced with sufficient precursors to complete, but which failed because of leaks, or gakks coating the phosphorous preventing recycling, it is more common to find intermediates and little if any pseudoepehdrine, as the the HI was present for a sufficient time to at least complete the first reduction. It did not complete because the HI fell too low during the reaction itself as the red got dirty and was ineffective to cause the I2 to be recycled. The HI level falls too low to drive the second reduction, although the first reduction is very close to complete.
When one finds pseudo in large percentages in the final product, the reaction was doomed from the start, as it never had sufficient HI to complete. Most incomplete reactions that contain intermediates but no noticeable pseudo suggest a mid-reaction failure from an otherwise sufficient inital soup.
Or that is how I have it figured, for what its worth.