In the segment parser loop three states are defined:

http://w3c.github.io/media-source/index.html#sourcebuffer-waiting-for-segment
WAITING_FOR_SEGMENT     Waiting for the start of an initialization segment or media segment to be appended.
PARSING_INIT_SEGMENT     Currently parsing an initialization segment.
PARSING_MEDIA_SEGMENT     Currently parsing a media segment.


Now you can't go from the WAITING_FOR_SEGMENT state to PARSING_MEDIA_SEGMENT state unless the "first initialization segment received flag" (http://w3c.github.io/media-source/index.html#first-init-segment-received-flag) is true.

Now consider the following situation.

1. sb.appendBuffer(init_segment1);
2. sb.appendBuffer(media_segment1);
3. sb.appendBuffer(invalid_init_segment2);
4. sb.appendBuffer(media_segment2);

In 1. The init segment is valid, and the first initialization segment received flag is set to true
In 2. Coded Frame Processing algorithm is run and frames are added to the trackbuffers.
In 3. will have the sourcebuffer throw an "error" event, and the mediasource state is changed to "ended" as per the "Append Error Algorithm".
The append state is reset back to WAITING_FOR_SEGMENT

Now come step 4. We move from WAITING_FOR_SEGMENT to PARSING_MEDIA_SEGMENT ; the frames are then inserted into their respective trackbuffers. Even though, no corresponding init segment has been appended ; which would result in unplayable frames stored in the trackbuffer.

Suggestion ; when an error is encountered, clear the "first initialization segment received flag" or much better specify that you must enter a new valid init segment and until then no new media segment can be appended.
This could be done by adding a new append state: WAITING_FOR_INIT_SEGMENT which is the initial append state

It would go like so:
WAITING_FOR_INIT_SEGMENT -> PARSING_INIT_SEGMENT -> WAITING_FOR_SEGMENT -> PARSING_MEDIA_SEGMENT | PARSING_INIT_SEGMENT

And should an error occur in the Initialization Segment Received algorithm (http://w3c.github.io/media-source/index.html#sourcebuffer-init-segment-received) or if the segment parser loop rejected an invalid init segment the append state would be set back to WAITING_FOR_INIT_SEGMENT