Some limitations of the MiniDisc format:

• Sometimes, the beginnings and endings of recorded tracks will have dead-air on them or will be slightly cut off. This is usually due to imperfect track-marking on a CD or glitches in an analog source. It's good to scan newly recorded tracks for imperfections, but dead air can be precisely removed using track divide/delete functions. If a track's beginning is cut off, you can just turn off the CD player's programming and record it manually.
• With all but the latest or most expensive decks you can't fade songs in or out unless you are using analog mode. Some CDs have their tracks merged together and digital gain control is ideal for fading harsh beginnings and endings. If your deck lacks digital gain control you can dub those particular tracks in analog and the rest in digital. Some people say they can't hear a difference between the two modes. If you absolutely don't want to use analog you can make a seamless divide/splice between two tracks. It may be barely noticeable if the timing is right.
• Unless you have a professional unit, you can't make pristine copies from one MiniDisc recorder to another because ATRAC creates subtle generational loss (cassettes are much worse in that regard). In any event, the law requires built-in SCMS protection on most digital recording equipment, making it hard to do multi-generation copies in the first place.
• A big part of the MiniDisc's strength is its non-linear editing capability, which uses a memory buffer to allow pieces of a single track to be read from various locations on the disc. This has minor downsides, though. If you delete tracks, change track numbers or clean up the beginnings/endings of several tracks, space will be freed up for new tracks, but it will be physically scattered on the disc. All of the above can cause audible noise in quiet environments as the read-head zips all over picking up the segments. Also if a disc is highly segmented you may run into "rehearsal" glitches when you try to divide tracks near the boundaries of separate data areas. In practice these are minor issues, but whenever possible it's best to record tracks in the order you want them and save editing for when it's needed.
• Scanning forward or backward to a specific point on a track is not as smooth or precise as it is with a CD. The small size of MiniDiscs probably accounts for this. Data scattered on different parts of the disc after editing may also cause small lags when scanning.
• MiniDisc labels are too small to allow hand-printing of numerous track titles unless you've got very fine dexterity. Using a computer to print the labels is almost mandatory. Several outfits sell blank labels for inkjet and laser printers. Certain Avery-style labels fit the disc sleeves well. I wish the sleeve (for Sony discs at least) had been designed with a slot for an edge-label. The one on the disc itself is only 3.5mm wide and can be hard to read when one eye is on traffic.