According to the Babylon 5 wiki
Babylons 1 through 3 were all destroyed during their construction by acts of sabotage.
Who were the saboteurs and what was their agenda?
The most specific information I could find on the sabotage of Babylons 1-3 states:
Babylon 1, originally known simply as the Babylon Station, was the first space station built by the Earth Alliance under the aegis of the Babylon Project. During construction, Babylon 1's infrastructure collapsed and exploded as a result of sabotage.
The second attempted station in the Babylon Project, Babylon 2 was also sabotaged and destroyed, exploding during construction.
Like the previous two stations, Babylon 3 was also sabotaged and destroyed, exploding during construction.
Unfortunately, this gives no indication of what group, or even what species was responsible for sabotaging the stations, or what motivation they had for doing so.
Update We have these additional lines in the episode Grail from Thomas Jordan, aka Jinxo, who worked on the construction of all 5 Babylon stations:
I worked a few months, took some leave and the station's infrastructure collapsed. Sabotaged. They never found out who. I remember. So I went to work on the second one. The firm still owned my contract. I took leave a second time and that station was sabotaged. And then when B3 blew up, well, that's when I got the name Jinxo.
This doesn't give us much information about who was responsible, however, it does suggest that at least to Jinxo's knowledge the culprits of the sabotage of Babylon 1 were never found. This makes it look less likely that there is a canon answer to this...