I know that was odd, it was split up just fine on the DVD
Just got my Serial Experiments Lain set today and there are a few things that really piss me off about it-this is supposed to be a "super deluxe set" but crapamation is using those lovely "cut out" cases that provide zero protection for the discs inside-and I don't mind them putting all 13 episodes on 2 blurays but how about evening up the episode count between the 2 discs-like 6 on one and 7 on the other instead of 9 on one and 4 on the other?
That's because of the layers. Dual layered Blu-ray Discs (50GB) cost much more money to make than single layered BD (25GB). The cost difference is by a dollar or two. This information came from David Williams from Sentai.
Almost all of Funimation and Sentai releases that contain 12-13 episodes have one dual layered BD (first disc) and one single layered BD. If there are 14+ episodes, then they will use 2 dual layered BDs (see Sekirei season 2, DTB season 2/w OVA or HLP season 1 for examples).
The cost between a dual layered DVD (about 8GB) compared to single layered DVD (about 4GB) is only a few cents difference. This is why almost all DVDs these days are dual layered.